Photoluminescence (PL) spectra and AFM measurements of InAs quantum dots grown in a site-selective manner on pre-patterned GaAs substrates are presented. A number of processing steps are described including a Ga-assisted deoxidation step to remove native oxides from the sample surface. Furthermore, post growth annealing is shown to be a promising technique for improving the quantum dot density and likelihood of single site-selective nucleation. Morphological transitions are shown to occur during the annealing process with two initial quantum dots in a given nucleation site transforming into one slightly larger quantum dot. Density measurements performed by AFM combined with PL spectroscopic measurements show that we have achieved optically active, site-selective dot growth, and additionally allow us to calculate that our site-selective dots are on average 30% as efficient as unpatterned dots.