In most cases, local power structures continued to exist. As with defeating the Mexica in the first place, Spain's colonial administration relied heavily on the existing pre-columbian political economy. At that time, like in other feudal societies, the means of production consisted chiefly of peasant communities (called altepetl) ruled by a local military and religious authority which collected tribute and paid some of it (raw goods, sometimes slaves) on to a larger polity like the Mexica (also called Aztrcs) or the Tarascans. At the time of Spanish conquest, the Mexica were well established as the dominant military entity in the region and collected tribute and sacrificial captives from most other states in the area. In most cases, Spanish imperial forces simply supplanted the Mexica after defeating them, continuing to collect tribute, in some cases from the very same individuals or families who had done this under Mexica rule (by then known as caciques, a word/concept of taino origin that the spanish adopted and applied all over Latin America, a local indigenous or mestizo leader who collects tribute and represents spanish interests (chiefly labor levies for infrastructure projects). While Spanish activity was indeed disruptive, many parts of central America became spanish imperial subjects without having any permanent residents of European descent or any serious disruption of their way of life. Over time, smallpox (eliminating an estimated 90% of people throughout the americas) did more to dismantle precolumbian city-states than individual conquistadors ever could have. Good further reading and my source for most of this information is Bradley Benton's book the Lord's of Tetzcoco.