The growth of submonolayer metallic or molecular nanostructures via ion-beam sputtering onto reconstructed semiconductor surfaces, followed by in-situ scanning probe imaging of the formed nanostructures, give an interesting insight into developing new molecular multifunctional nanoarchitectured materials for various applications. The case of pentacene, as one of the most important candidates in the field of organic thin lm electronics, molecules and also Au metallic nanostructures, deposited in the submonolayer regime onto a reconstructed InP (0 0 1) surface, is discussed in view of the observed growth modes, structure and topology. During initial stages of growth, a uniaxial di usion channel dominates, and long pentacene molecular chains self-organize parallel to the [110] crystallographic direction on the InP surface. The study is performed by in-situ non-contact atomic force microscopy investigations with atomic resolution. It is shown that the self-assembling of molecular structures onto at terraces is dependent on the atness and orientation of the terraces reconstructed onto the semiconductor surface. Moreover, it is possible to create functional molecular nano-architectures by nano-manipulation of single molecules with the AFM tip. This procedure may have a large impact on technological applications, such as organic TFT and molecular nanowires.