To answer your question briefly Charles army did not loose to the Swiss pike formation directly. Charles army lost because of poor military intelligence and being caught unaware at the battle of Grandson and Morat, and in the final battle of Nancy being outmaneuvered when the enemy army had a good idea of how his troops would be set up by using military intelligence which allowed them to prepare accordingly for the battle.

Battle of Grandson

Lost because of poor military intelligence on the enemy and an order which caused his men to route.

" On 2 March 1476 the Swiss army approached the forces of Charles near the town of Concise. The Swiss, eager to avenge their slaughtered countrymen, advanced in three heavy columns, echeloned to the left rear, moving directly into combat without deploying, in typical Swiss fashion. Poor reconnaissance left Charles uninformed as to the size and deployment of the Swiss, and he believed that the Swiss vanguard was the entire force sent against him. The vanguard, consisting mainly of men from Schwyz, Bern, and Solothurn, realized they would soon be in battle and knelt to pray. When they said three Our Fathers and three Hail Marys, some of the Burgundian army reportedly mistook their actions as a sign of submission. In their zeal, they rode forward shouting, "You will get no mercy; you must all die." The Burgundian knights soon surrounded the Swiss vanguard, but then Charles made a serious mistake. After brief skirmishing, Charles ordered his cavalry to pull back so the artillery could reduce the Swiss forces before the attacks were renewed. At this time, the main body of the Swiss emerged from a forest which had hitherto obscured their approach. The Burgundian army, already pulling back, soon became confused when the second, and larger, body of Swiss troops appeared. The speed of the Swiss advance did not give the Burgundians time to make much use of their artillery and missile units. Charles attempted a double envelopment of the leading Swiss column before the other two arrived, but as his troops were caught shifting to make this attack, they caught sight of the other Swiss columns and retreated in panic. The withdrawal soon turned into a rout when the Burgundian army broke ranks and ran. For a time, Charles rode among them shouting orders for them to stop and hitting fleeing soldiers with the flat of his sword. But once started the rout was unstoppable, and Charles was forced to flee as well. Few casualties were suffered on either side: the Swiss did not have the cavalry necessary to chase the Burgundians far. At insignificant cost to themselves, the Swiss had humiliated the greatest duke in Europe, defeated one of the most feared armies, and taken a most impressive amount of treasure. The booty Charles carried with him was immense, and included jewellery, silver and gold plate, tapestries and much of Charles' artillery. The Swiss initially had little idea of its value."

source - Florens Deuchler, Die Burgunderbeute

Battle of Morat

Lost because his army was in disarray when the attack came. Again low military intelligence lost him the battle since he did not see the enemy coming even though he knew where they would attack from. His troops were getting paid, eating, and staying out of the rain when the Swiss army attacked. His perfectly laid battle plan was not able to come into effect because of his army being in disarray.

Preparation:

"Charles in the meantime had been kept reasonably well informed of the approach of the Confederate army, though he did nothing to hinder their approach. This is not to say that he was unprepared for the arrival of the Swiss; indeed in typical fashion Charles had prepared an elaborate plan to meet the enemy on ground of his choosing where he thought they would approach from some 2 km (1.2 mi) from Murten. The terrain around Murten is quite hilly and he had chosen to rest his left flank artillery on a steeply sloped gorge cut by the Burggraben stream. In the centre, behind an elaborate ditch and palisade entrenchment known as the Grunhag, stood the bulk of Charles’ infantry and artillery not engaged in besieging Murten itself. These were to fight the Confederation pike and halberd blocks to a halt while on the right the massed Gendarmes would then flank the frontally engaged Swiss, thus creating a killing ground from which there was no escape.

On June 21, 1476, Charles expected the Confederation forces to attack. He arraigned his armies and prepared for the coming assault. However, the Confederation leadership decided to wait an additional day for the troops from Zürich. After about six hours of waiting Charles ordered his troops to stand down and return to camp."

Caught Unaware

"around mid-morning, Charles ordered his treasurer to pay the entire army, expecting the Confederate troops to continue delaying. The orderly lines of the Burgundian army dissolved into chaos as soldiers scattered throughout the camp collecting their pay, eating their midday meal and seeking shelter from the rain. The skeleton force that remained at the Grunhag were surprised when the Swiss army, in battle order, emerged from the woods less than 1,000 m (1,100 yd) from their lines.The Confederate Vanguard of some 6,000 skirmishers and all the 1,200 cavalry present erupted out of Birchenwald Woods to the west of Murten, exactly where Charles had predicted they would appear.

Behind the Vanguard came the main body of pike, the Gewalthut (Centre). This was some 10,000 to 12,000 strong and was formed in a huge wedge with the cantonial standards in the centre, flanked by halberdiers and an outer ring of pikemen. The Rearguard of 6,000 to 8,000 more closely packed pike and halberdiers followed the Gewalthut towards the now sparsely manned Grunhag.

As the Swiss charged downhill into the Burgundian position the artillery managed to fire a few salvoes, killing or maiming several hundred of the overeager Lorrainers. Against the odds the defenders in the Grunhag held the Swiss for some time before a contingent of Swiss found a way through the left flank of the defences near the Burggraben and turned the whole position. The Swiss formed up quickly beyond it and advanced towards Murten and the besieger’s camp.

In the Burgundian camp all hell was let loose once the Swiss were sighted as men rushed to reform and prepare for battle. In the ducal tent on top of the Bois Du Domingue, a hill overlooking Murten, Charles was quickly armed by his retainers before rushing on horseback to try to coordinate the defence of the camp. But as fast as any unit was formed and moved forward against the Swiss, it was swept aside as various uncoordinated attacks were made against the still compact Confederate battle formations. There was some resistance from the squadrons of the Ducal household who routed the Lorrainers, including René II, Duke of Lorraine, who was saved only by the arrival of the pikes, against which the Gendarmes could only retire, unable to make any impression against them.

Charles managed to muster enough English archers to form a last line of defence before the camp, but these were routed before a bow could be bent, their commander shot by a Swiss skirmisher. Traditionally, the Duke of Somerset is identified as the commander of the English archers. However, the only Duke of Somerset, Edmund Beaufort who was known to have been in Burgundian service died in 1471 at Tewkesbury in England and therefore could not have been at Murten five years later.Then it was every man for himself as Charles ordered the army to fall back which was interpreted as a retreat, which in turn became a rout as all organized resistance ended.

For some three miles along the lakeside many Burgundians died that day in the rout. The Italian division of some 4,000–6,000 men besieging the southern part of Murten probably suffered the worst fate: cut off by the Swiss rearguard and attacked by a sally from the town, they were hunted down along the shore and driven into the lake. As promised, no quarter was granted.

More fortunate was the Savoyard division under Jacques of Savoy, Count of Romont which was posted in the northern half of the Murten siege works. Forming up and abandoning all their baggage they retreated east round the lake and eventually made good their escape to Romont (one of Jacques' lesser titles was count of Romont)."

Source - Vaughan, Richard (2002). Charles the Bold : the last Valois Duke of Burgundy.

Battle of Nance

Enemy had a good idea of how Charles troops were set up and realized that a full frontal attack would loose them the battle. They then laid out a good battle plan that won them the battle.

Final battle that Charles died in.

Preperation

"If Charles suffered from a lack of scouting (which had cost him so dearly at Murten six months earlier), the same could not be said for the Allied army. Despite the driving snow cutting visibility to a few yards, the Allied scouts soon recognized that a frontal assault on the Burgundian position would be disastrous. The largely Swiss Vorhut (Vanguard) of 7,000 infantry and 2,000 cavalry, were instructed to attack from the right, while the principal thrust would come from the 8,000 infantry and 1,300 cavalry of the Gewalthut (Centre), which was dispatched on a difficult circuitous march round the left flank, over thickly wooded snow-covered slopes out of view of the waiting Burgundians. The small Nachhut (Rearguard) of 800 handgunners acted as a reserve."

The Battle

"After a march lasting some two hours, the Gewalthut emerged from the wooded slopes slightly to the rear of the Burgundian position and formed up in a wedge formation. The early notes of the Swiss horns sounded thrice, and the Swiss charged downhill into the Burgundian positions. The artillery attempted to retrain on the Gewalthut but could not elevate enough to be effective; the single volley discharged killing but two men. Although the right wing Burgundian cavalry saw off their Swiss rivals, the mass of Swiss infantry pushed on to engage the outnumbered Burgundian infantry square in a one-sided fight. The Vorhut threw back the Burgundian left wing and put the artillery to flight. As Charles attempted vainly to stem the Gewalthut's advance by transferring troops from his left flank, the sheer weight of numbers arrayed against him became obvious, and the once proud army of the Duchy of Burgundy started to melt away in flight.

Determined to the last, Charles and his staff tried in vain to rally the broken army, but without success. His small band was carried with the flight until eventually surrounded by a party of Swiss. A halberdier quickly swung at the Duke's head and landed a deadly blow directly on his helmet. He was seen to fall but the battle flowed on around him. It was three days until the Duke's disfigured body was finally found and positively identified amongst the detritus of the slaughter. So passed the last of the Valois Dukes of Burgundy."

Source: John Foster Kirk (1868). History of Charles the Bold, Duke of Burgundy. J.B. Lippincott & Co. p. 537–542.