The molecular arrangement of copper phthalocyanine (CuPc) on atomically flat Si(001)-(2 × 1)-H was studied with atomic force microscopy and complimentary techniques. Images obtained on 10–20 nm thick films indicate that the column of stacked molecules lie parallel to the surface, in contrast to the case on flat Si(111)-(1 × 1)-H where the column stands perpendicular to the surface. The lateral spacing was estimated to be 1.33 ± 0.05 nm and the spacing of the molecular layers to be 1.18 ± 0.01 nm, which agree approximately with a2 and c2 of the α-form CuPc crystal, respectively. High-resolution frictional force images of the crystal show periodic rows of alternate higher and lower friction peaks, which correspond to two benzene-ring rows in a column with different heights. The orientation of the crystal was also different from that on relatively rough Si(001)-H.