I am afraid that I cannot help with the solidworks slicing as I do not use 3d, but I do make a lot of small scale models for our miniatures. The system that I use to ensure perfect alignment is to drill 2 or 3 2.01 mm holes through each layer for location dowels and 2mm cocktail sticks for the dowels (the sticks from our local coop are just about 2mm spot on). I never use a drill bit, but rout out the holes to whatever size hole I need (on larger items I use bigger dia dowels). G.