To design and fabricate next-generation tissue engineering materials, the understanding of cell responses to material surfaces is required. Surface topography presents powerful cues for cells and can strongly influence cell morphology, adhesion, and proliferation, but the mechanisms mediating this cell response remain unclear. In this report, we have investigated the effects of nanoroughness assemblies of silk fibroin protein membranes and RGD sequences fabricated from two different silk fibroin sources, that is, mulberry (Bombyx mori) and nonmulberry (Antheraea mylitta), on cytoskeletal organization, proliferation, and viability using primary rat bone marrow cells. To vary surface roughness, silk fibroin substrates were treated with graded ethanol (50%-100% v/v) to produce nanoarchitectures in the range of 1-12 nm height. The graded alcohol treatments have been found to produce nanoscale topographies of reproducible height in a much faster and cheaper way. The results showed no difference in cell proliferation within the same treatment groups for both silk types. However, a change in cell response in terms of good cytoskeleton organization, actin development, cell spreading, and strong binding to substratum using A. mylitta fibroin protein films having RGD sequences was observed. This finding provides the information that the nanoroughness affects cellular processes in a cell-specific manner and may be helpful for the development of smart silk-based biomaterials especially for directing cell differentiation and regenerative therapies.