How do I set the floor in the middle of the tile?

If that makes sense.

I want to change my floors from a flat surface to a 3d-lego style block such that when the player is on the tile, he actually appears to overlap the top part of it.

This might be a poor example, but say consider the wooden platform here is a tile, and the character is running/standing in the "middle" of it.

A sample or something would be great, I can't seem to find what I'm looking for.

This was achieved by simply blocking the level geometry in with invisible collision sprites, the actual artwork itself is just window dressing.

You can either use this technique or alter your artworks collision polygon in the sprite editor to fit your purpose.

Thanks that makes sense ... had a bit of a brain lock.