We use a two-photon laser-scanning microscope to fabricate two-dimensional (2D) photonic crystal structures in commercially available SU-8 polymer films, and successfully demonstrate making nanostructures beyond the diffraction limit with high aspect ratios. By varying the laser beam power, scanning speed, focal depth, line spacing and scanning angles, we obtain 2D photonic crystals with circular, elliptical, rectangular, or diamond-shape unit cells in a hexagonal or square lattice. An aspect ratio as high as 6.9 with 250 nm line width was achieved. In addition, we can controllably place defects of specific patterns, e.g. lines, dots, and Y-splitters, in the otherwise perfect photonic crystal. We also combine two-photon nanolithography with conventional UV photolithography to make 2D photonic crystals between waveguides. The combination of these two lithography methods was done on a single polymer film, suggesting potential for easy fabrication of complex photonic devices.