A III-V semiconductor photonic crystal (PhC) waveguide is integrated into a semiconductor optical amplifier (SOA); this has the potential to reshape pulses that are distorted and chirped on propagation through the SOA. The PhC waveguide is modeled using the three-dimensional (3D) finite difference time domain (FDTD) method initially for the ideal case of infinite depth holes, and this shows a ministop band close to 1600 nm. The PhC waveguide is then fabricated into a commercial SOA using focused ion beam etching. The optical power measured at the output of the PhC-SOA waveguide shows evidence of a ministop band but with a small stopband depth. More realistic 3D FDTD modeling including effects of finite hole depth and vertical layer structure is then shown to give much better agreement with measured results. Finally predictions are made for the performance of a membrane structure.