If you use eagle, you can find a CAM script that will export the right layers here.
If you use Fritzing, select File -> Export -> For Production -> Extended Gerber and select a directory for the resulting files. Upload the file named your_project_contour.gm1 for the outline and your_project_pasteMaskTop.gtp for the paste layer.
This site is untested, unfinished, unpolished and unlikely to work for anything serious. Good luck.
See bottom of the page for some usage hints.
Special thanks to kazade for the brilliant idea of using OpenSCAD to make this work. This app uses pcb-tools to read Gerber files and SolidPython to generate OpenSCAD code. OpenSCAD is used to generate the resulting STL files. The website is built using Django.
You can find the code for the underlying converter at https://github.com/kirberich/gerber_to_scad. The code for the web app can be found at https://github.com/kirberich/gerber_to_scad_service.