In this study, cell responses on micropatterned films that were changing in groove–ridge widths and pattern depth were investigated to compare the degree of size effects from X–Y and Z planes. Poly(caprolactone) films with five different groove–ridge sizes and three pattern depths were prepared by hot embossing technique. In general, the morphologies of osteoblast cell were not changed noticeably by the size changes in groove–ridges with the same depth size. However, cell morphologies were changed significantly when pattern depths were increased from 1.35 to 4.95 µm. Also, the cell morphology change between different groove–ridges was significant when the pattern depth was small (1.35 µm), and these effects were diminished or masked when the pattern depth was increased to 4.95 µm. Linear regression analysis further clarifies that unit size changes in depth may affect cell length and orientation rates 2.4 and 4 times, respectively, in comparison to rates obtained from X–Y planes.