I'm not a frame builder but have had several custom bikes made. Loosely speaking, the process has been the same each time: to take a whole lot of body measurements, ask a lot of questions about what I'm looking for and what kind of riding I plan to do on the bike (racing, touring, ...). The frame builder then takes all of this and the output is a frame design (tube types, tube lengths, angles, bb height, etc) that hopefully both fits and does what I want it to do.
I'm curious how frame builders do this. Do you all use a software tool, "rule of thumb" or some other mechanism to come up with a frame design?