Surface slip was employed to control flow separation induced by small-scale Gaussian-shaped surface deformations on a two-dimensional flat plate. Single surface deformations, including bumps and gaps, were modelled, which generated separated flow along the rear side of the bump and within the gap concavity for a Reynolds number Re = 100 000 when the plate surface was subject to the no-slip condition. Surface slip was modelled using a Navier-slip condition and quantified by a slip length, λ. Bump deformations had a greater impact on the flow dynamics than gap concavities, generating more intense regions of reversed flow and requiring larger slip lengths to inhibit flow separation. In addition, double-bump configurations were modelled, with the location of the two bumps playing a critical role in the evolution of the flow. When the bumps were close together, the first bump controlled the size of the separation bubble that developed downstream of the second bump. Whereas when bumps were far apart, a moderate slip length, λ, excited nonlinear oscillatory flow, reminiscent of the low-frequency flapping observed in previous studies [1][2][3]. However, increasing the slip length suppressed this phenomenon and ultimately eliminated all pockets of separated flow.