Sure, the most famous example is the Coronado expedition which came up through Mexico and went into the Great Plains/Arkansas River Valley area.

The Spanish were looking for gold and sacked a number of Native Villages along the way. However, their "guide" had hopes of getting them lost in the plains and he succeeded. The Spanish found no gold and had to return to Mexico heavily depleted from constant skirmishes. This ushered in a "century of darkness", where there were no more European records from the region until the 17th century.

Now were the Native Americans ever able to completely stop European Settlers? This question is not answerable. The Europeans lost sometimes and the Natives won sometimes, however you have to remember that Natives (or Europeans for that matter) were never a unified a front. In the early days Natives in some areas welcomed Europeans and would play the Europeans against their own enemies, making them a tool. Plus the technology Europeans brought would provide an advantage to Natives.

And then you have European powers who curry favor with Natives to gain them as ally against other European and Native enemies.

Now, if every Native tribe gathered together and made coordinated efforts to stop Europeans then there is no doubt in my mind they could have. You are talking about 100 settlers vs. thousands of Natives. But this isn't the way Native/Colonial politics worked at all.

Sources:

Richard White, The Middle Ground Kathleen Duval, The Native Ground

http://en.wikipedia.org/wiki/Francisco_V%C3%A1squez_de_Coronado#The_Search_for_Quivira

One of the closest-run cases is King Philip's War, in 1675. I recommend this book if you're interested in learning more. By percentage of population, it was the bloodiest war of the colonial era, and some historians have argued that it spelled the end of Puritan independence and paved the way for later incorporation into Massachusetts colony. I'd argue that the continued influx of non-Puritan English settlers was more to blame, but there you are.

Overall, however, the theme is one of occasional local successes but a lost cause, even in the West. Disease and the inability of tribes to unite against the Europeans tended to be too much when combined with superior logistics.

The vikings essentially lost Vinland to the native Americans. Thorfinn Karlsefni tried to colonize Vinland with three ships and 140 men. After several skirmishes where the technological superior vikings won and "slew many of the natives", Thorfinn still concluded that "despite everything the land had to offer there, they would be under constant threat of attack from its prior inhabitants".

They thus returned to Greenland.

Source "Saga of Erik the Red"

(*edit: cause i actually do know what an adverb is)