Do you have some examples of what you're talking about?

As is, it's hard to provide an answer because Aztec temples were quite frequently demolished Perhaps most notable was the destruction of the Templo Mayor of Tenochtitlan, which wasn't excavated until 1978 when some workers rediscovered it while installing a power transformer. Mexico City was built right on top of the old Aztec capital, so not much of it was "still standing." The oft-circulated reproduction by Juan Gómez de Trasmonte of a 1628 map shows many cathedrals and minimal Aztec influence. While it can't be considered a photograph, as it represents a more idealized, European vision of the city, that an artist would imagine the ideal Mexico City as one without visible Aztec temples says something itself.

On the other hand, in Cuzco, the Inca equivalent to Tenochtitlan, the Inca structures were often partially razed but then incorporated into Spanish buildings- as is quite visible at the Coricancha, which now supports the Iglesia y Convcento de Santo Domingo. Inca walls still line many Cuzco streets.

While there is certainly a lot to be said about Spanish engagement with indigenous architecture, there's no answer to your question as is. Inca structures were not always reduced to ruins, and Aztec structures were quite frequently leveled. Were there any specific temples or cities that you pictured?

I'm mostly looking to see if there was a difference in the colonization practices of the Spaniards. Conquistadores intentionally destroyed temples in both societies, however, I'm wondering why they were successful in eradicating the Incan ones while leaving many Aztec and Mayan untouched.