Preparation of GaAs-based compliant substrates that utilize wafer bonding generally relies on integrated AlxGa1-xAs etch stop layers to provide the precise control required to stop selectively on GaAs layers less than 100 Angstrom thick We demonstrate that removing an Al0.7Ga0.3As etch stop layer with HF or HCl:H2O leaves the underlying GaAs layers with rns roughness of 10-20 Angstrom and peak-to-peak roughness of 65-150 Angstrom. Following the Al0.7Ga0.3As selective etch, the morphology of the underlying GaAs layer is improved with a wet chemical digital etch comprised of alternate soaks in H2O2 and HCl:H2O, which results in a GaAs surface with rms roughness of similar to 2 Angstrom and peak-to-peak roughness of similar to 20 Angstrom. Lattice-matched p(+)-n junctions deposited on thin-bonded GaAs substrates and test substrates that are prepared for growth using the digital etch have electrical characteristics comparable to those deposited on a hulk epi-ready GaAs substrates. However, similar lattice-mismatched In0.2Ga0.8As p(+)-n junctions deposited on the thin-bonded GaAs substrates and test substrates have dark currents that are more than an order of magnitude higher than those deposited on bulk epi-ready GaAs substrates. These results suggest that despite the smoothing of the digital etch, the material that remains on the surface of the thin GaAs layer is responsible for the degradation observed in the lattice-mismatched devices deposited on the thin-bonded GaAs substrates.