CaseMaker.com is a nice tool to make boxes with, but the settings has to be right.
I have been experimenting with CaseMaker, and how to find the perfect kurf for a 3 mm acrylic box.
This is my findings.
The kerf is the material that is cutted off to make the tabs fit together. After you click Generate Laser Cutter Case Plans, you can type in a Laser Cutting Kerf. The best fitting for a 3 mm acrylic box, was found to be 0.08. Another finding that's worth mentioning, is that the tabs sometimes aren't fitting right after cutting, but will fit after 30-60 minutes.
Customize holes for tabs:
CaseMaker will only make tabs for you on the edges of a plate, but let's say that you want to make tabs fit on the middle of a plate (like the picture above). Copy your plate with tabs in Inkscape. Delete the plate, so that it's only the tabs left. Transform the tabs into squares (your holes). These holes will then be the exact same size as your tabs - but then the tabs will be too large to fit in the holes. The lenght of the holes will be fine, but the hight has to be adjusted. Select all your holes, and click Object -> Transform. Set the hight to 103% in the Scale option. Now they should fit.
See the attached zip (svg) file.
Maybe these settings won't work perfectly for every project, but they will give you a start to find the perfect kerf and hole size.