Walking through stuff on the second and third layers

My guy keeps walking through stuff on the second and third layers. How can I stop it? It's a little frustrating.

You've probably "painted" the top layer or second layer with a blank passable tile.

Grab an impassable tile that's not likely to be used on the top two layers, go to both of those layers, and "paint" in an open area.  Keep painting in open areas (use F4 to darken the other layers) until all the tiles are either painted with this temporary tile, or contain something that you really want there.  Then grab the top-left tile (should be blank if it's an outdoor area), and paint all that back out again.

Repeat for the next layer.

At least ... that's how I got myself into that problem and back out again.  It might depend on the tileset you're using too.

Either that, or you've set the passage in the tileset incorrectly.

If you've checked the passability of each tile then maybe your have accidentally blanked out using the wrong tile.

First, make sure the first tile on the tileset (blank) is set to a priority of 5, and passability of O.

Now, make sure that all blank tiles on all layers use the first tile. If you accidently used a different blank tile from your tileset then this will mess with the passability.

If you are not sure if a map tile is using the first tile or not, then edit your tileset so that all extra blank tiles have a big fat X on them (or some other identifiable graphic). Then they should show up clearly and you can and replace them with the first tile.