In this article we describe an in situ, low damage, process sequence designed to provide a more reliable, higher quality metal (superconductor)-semiconductor interface. We produce discrete Nb contacts on an InAs quantum well (125 Angstrom) that is embedded within thick (similar to 3000 Angstrom) Al0.5Ga0.5Sb barrier layers by utilizing a multichamber ultrahigh vacuum system, in which two Varian GenII, Molecular Beam Epitaxy chambers are directly connected to a high vacuum etch station. The principal process steps include (1) a short, "selective" thermal Cl-2 etch of the top barrier layer to expose and define the InAs contact region, (2) a post-etch anneal (under As-2 flux) to desorb residual etch products (i.e., InCl3) and restore a clean and well-ordered InAs (2x4) surface, (3) a Sb capping/passivation layer on the treated surface, (4) atmospheric transfer of the capped sample to a remote Nb deposition chamber, and (5) a post-anneal (in vacuum) to desorb the Sb cap immediately followed by Nb deposition. The priority throughout is minimizing damage and impurity exposure to the InAs surface. Morphology and roughness of the etched surface are explicitly considered in terms of the (1) initial native oxide removal: short Ar+ sputter at room temperature versus thermal desorption at 530 degrees C under Sb-2 flux, (2) thermal Cl-2 etch temperature (180-260 degrees C), and (3) annealing temperature for Sb desorption (430-530 degrees C).