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 a/2 and c/2 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.