A combination of atomic force nanolithography and metal organic vapor phase epitaxy has been used to control the nucleation of InAs nanostructures on InP substrates. Pits with controlled width and depth were produced on InP with the use of atomic force nanolithography. The number of nucleated nanostructures depends on the applied force and is independent of the geometry of the pits. Study shows that the density of crystalline defects introduced by nanoindentation is responsible for the number of nucleated nanostructures. © 2007 American Institute of Physics.