This contribution presents a stability analysis for compressible boundary layer flows over indented surfaces. Specifically, the effects of increasing depth D /δ * and Ma ∞ number on perturbation time-decay rates and spatial amplification factors are quantified and compared with those of an unindented configuration. The indented surfaces represent aeronautical lifting surfaces endowed with the smooth gap resulting when a filler material applied at the junction of leadingedge and wing-box components retracts upon its curing process. Since the configuration considered is such that the parallel/weakly-parallel assumptions are necessarily compromised, a global temporal stability analysis is considered in this study. Our analysis does not require a parallel flow constrain, and hence it is believed to be valid when two dimensional effects are relevant. We find that small surface modifications enhance certain flow instabilities. An increase in Ma ∞ enhances further this behaviour: for the D /δ * = 1.5, Ma ∞ = 0.5 case, amplification factors at a given location can be up to 20 times larger than those corresponding to the unindented case.