In order to develop nanoengineering methods to control electronic spectrum of self-assembled InAs quantum dots (QDs) grown by molecular beam epitaxy, we have utilized atomic force microscopy (AFM), photoluminescence (PL) and TEM methods to investigate the effects of capping layer growth on the physical/chemical properties as well as the optical/electronic performance of QD device structures. Capping layer material choice (or its absence all together) has been found to directly influence QD dimensions (size, height), and subsequently, to affect QD emission wavelength. We report results of QD lateral size and height as well as densities of InAs QDs capped with 2ML (monolayers) of AlAs or GaAs grown at various rates. Our AFM results are complemented by PL measurements, where the optical properties of capped versus non-capped QDs have been explored and direct correspondence between structural differences induced by capping and the electronic/optical properties of QDs is demonstrated. Analysis of the data shows that the results can be explained by two competing surface processes. The first of which is the redistribution of indium between QDs on top of the 2D wetting layer, resulting in the increase of QD size with time. The second effect is the diffusion of indium out of the QDs and onto the top of the capping layer. TEM with multislice image simulation has supported our AFM and PL observations with the demonstration of “indium driven” alloy intermixing in the overlayer as well as significant alloying in the InAs wetting layer.