The surface structure is known to significantly affect the long-range capillary forces between hydrophobic surfaces in aqueous solutions. It is, however, not clear how small depressions in the surface will affect the interaction. To clarify this, we have used the AFM colloidal probe technique to measure interactions between hydrophobic microstructured pore array surfaces and a hydrophobic colloidal probe. The pore array surfaces were designed to display two different pore spacings, 1.4 and 4.0 μm, each with four different pore depths ranging from 0.2 to 12.0 μm. Water contact angles measured on the pore array surfaces are lower than expected from the Cassie–Baxter and Wenzel models and not affected by the pore depth. This suggests that the position of the three-phase contact line, and not the interactions underneath the droplet, determines the contact angle. Confocal Raman microscopy was used to investigate whether water penetrates into the pores. This is of importance for capillary forces where both the movement of the three-phase contact line and the situation at the solid/liquid interface influence the stability of bridging cavities. By analyzing the shape of the force curves, we distinguish whether the cavity between the probe and the surfaces was formed on a flat part of the surface or in close proximity to a pore. The pore depth and pore spacing were both found to statistically influence the distance at which cavities form as surfaces approach each other and the distance at which cavities rupture during retraction.