It's the same as making a PCB board, you coat it with an etch resist etch away the parts you don't want and you're all set. There's a good chance that you could directly print a pattern onto Mylar and use an etch that will eat the Mylar but not the toner on both sides, but I'm not sure of the practicalities of that.
Another option is using punches to manually make masks. Solder paste will tend to reflow to the nearest soldering point so ribbons across, so even if you do a solid strip across the legs of an SMD component when it reflows it will avoid filling gaps all by itself as long as the available solder paste is low enough, you'll only get shorted legs if you use too thick or too wide of a mask.