The Shift-Key method helps with 3D construction using desks or cabinets as a foundation.
What I do: place Floor Tile in the area I want to build in. Put the base layer of cabinets down, then raise the floor tiles with SHIFT+Drag until the tile is over the first layer. Continue in this manner much like you would with Legos to assemble a structure.
For example with Cabinets, I use Rustic Cabinets with the last clear part of the cabinet bounding box overlapping into the prior one I put down to make a solid floor. After 4-5 cabinets high of column work, I can make a ceiling with the same cabinet to make a sub-floor. In this manner, it's easy to make 3 floors in a room with both floor and ceiling sections filled in, or up to 6-8 in a fully open room with nothing filled in.
The cabinets are the hardest, most tedious part. But other considerations come into play, such as lighting. Cabinet Ceilings are not actual ceilings, so lighting will be a challenge to place. You need to cheat with wall lighting at places where you can get away with it. Then there's navigation: ideally a ramp or staircase will need to exist to reach a higher floor without travel powers on. (There's no right answer for stairs: not every staircase is linear, and making a round one out of square stairs and 'floor' blocks can be a challenge.)
But with that, layered construction is much easier than relying on magic desks, lamps or safes.