Grimrock

So I'm wanting to make it so I have a "tunnel" that goes thru one of the raised up parts of the flooring. Is that possible and if so how?

Example being: Floor set 1, height set 3, and in the same position having a hallway or tunnel that would be floor set 0, height set 3.

Yes it is possible. You have to build the upper level out of entities map parts. Watch Skuggasveinn's tutorial part 2

Emera Nova wrote:Example being: Floor set 1, height set 3, and in the same position having a hallway or tunnel that would be floor set 0, height set 3.

Not the way you describe it. You need

floor 0 + ceiling 3
then
height 1 or 2 bridge
or
height 0 fake ceiling + height 1 fake wall
height 2 invisible platform + fake floor
etc

each tile only has one base floor and ceiling, use objects for rest