This article presents results for the optical characterization of two-dimensional photonic crystals (PhCs) in silicon-on-insulator fabricated using focused ion beam (FIB) etching. A detailed description of fabrication techniques is given and the use of gas assisted etching for large area etches is outlined. The optical characterization shows PhC band edges at the expected wavelengths but with reduced depth. Three dimensional finite difference time domain modeling is used to investigate this discrepancy and this suggests that reduced sidewall verticality is not critical in this strong vertical guiding regime. Other possible explanations for reduced band edge depth are discussed including gallium implantation and FIB induced optical damage. (c) 2006 American Vacuum Society.