A rapid predictive tool based on the linearised Reynolds-averaged Navier–Stokes equations is proposed in this work to investigate secondary currents generated by streamwise-independent surface topography modulations in turbulent channel flow. The tool is derived by coupling the Reynolds-averaged momentum equation to the Spalart–Allmaras transport equation for the turbulent eddy viscosity, using a nonlinear constitutive relation for the Reynolds stresses to capture correctly secondary motions. Linearised equations, describing the steady flow response to arbitrary surface modulations, are derived by assuming that surface modulations are shallow. Since the equations are linear, the superposition principle holds and the flow response induced by an arbitrary modulation can be obtained by combining appropriately the elementary responses obtained over sinusoidal modulations at multiple spanwise length scales. The tool permits a rapid exploration of large parameter spaces characterising structured surface topographies previously examined in the literature. Here, channels with sinusoidal walls and with longitudinal rectangular ridges are considered. For sinusoidal walls, a large response is observed at two spanwise wavelengths scaling in inner and outer units respectively, mirroring the amplification mechanisms in turbulent shear flows observed from transient growth analysis. For longitudinal rectangular ridges, the model suggests that the analysis of the response and the interpretation of the topology of secondary structures is facilitated when the ridge width and the gap between ridges are used instead of other combinations proposed in the literature.