We study theoretically and experimentally pressure-driven flow between a flat wall and a parallel corrugated wall, a design used widely in microfluidics for low-Reynolds-number mixing and particle separation. In contrast to previous work, which focuses on recirculating helicoidal flows along the microfluidic channel that result from its confining lateral walls, we study the three-dimensional pressure and flow fields and trajectories of tracer particles at the scale of each corrugation. Employing a perturbation approach for small surface roughness, we find that anisotropic pressure gradients generated by the surface corrugations, which are tilted with respect to the applied pressure gradient, drive transverse flows. We measure experimentally the flow fields using particle image velocimetry and quantify the effect of the ratio of the surface wavelength to the channel height on the transverse flows. Further, we track tracer particles moving near the surface structures and observe three-dimensional skewed helical trajectories. Projecting the helical motion to two dimensions reveals oscillatory near-surface motion with an overall drift along the surface corrugations, reminiscent of earlier experimental observations and independent of the secondary helical flows that are induced by confining lateral walls. Finally, we quantify the hydrodynamically induced drift transverse to the mean flow direction as a function of distance to the surface and the wavelength of the surface corrugations.