A high quality finished prototype aircraft or other composite part is manufactured using a low temperature limit male mold, a cured female tool, and an at least partially automated layup process, and then touched up by hand to meet a tolerance or other specification. The female tool is preferably made from a male mold, by depositing layers of composite material over the mold, curing the tool together at a first cure temperature, separating the tool and mold, and then curing the tool at a second, higher temperature. The first cure temperature should be at or below an upper limit temperature no greater than 180° F. The second cure temperature is preferably in the range of 250° F. to 350° F. The step of hand touching up can comprise one or more of mechanically abrading and deforming a first portion of the composite part to mate with a second portion of a composite part.