We report on the optimization of nanostructured copper phthalocyanine (CuPc) thin films for idealized organic photovoltaic (OPV) architectures using advanced substrate motion and periodic seeding. Oblique angle deposition (OAD), a subset of glancing angle deposition (GLAD), has recently been used to enhance small molecule OPV device photoconversion efficiency by increasing the surface area of metal phthalocyanine (MPc) thin films. Here we report a detailed study of how to direct MPc film growth towards the ideal donor morphology using the techniques available to GLAD. Porous films of columnar CuPc nanostructures were achieved with strong control over the diameter, spacing and height of the columns. Special emphasis was placed on limiting column broadening as the film thickness, and resulting light absorption, was increased. Columns were grown on PEDOT:PSS coated ITO substrates to hundreds of nanometers in length while maintaining diameters of 40–50 nm and crystal grain sizes of 15–30 nm. Additionally, we provide the first demonstration of periodically seeded organic nanocolumn growth. These methods enable fabrication of uniform columnar MPc films engineered specifically for the short exciton diffusion lengths in these materials, making them suitable for ideal OPV device geometries.