The controlled 3D nanostructuration of molecular layers of the semiconducting molecules C₂₂H₁₄(pentacene) and N,N′-dioctyl-3,4,9,10-perylene tetracarboxylic diimide (PTCDI-C8) is addressed. A tip-assisted method using atomic force microscopy (AFM) is developed for removing part of the organic material and relocating it in up to six layer thick nanostructures. Moreover, unconventional molecular scale imaging combining diverse friction force microscopy modes reveals the stacking sequence of the piled layers. In particular, we unambiguously achieve epitaxial growth, an issue of fundamental importance in thin film strategies for the nanostructuration of more efficient organic nanodevices.