Cyclohexane is confined between two surfaces. Different types of confinement geometries are realized using different preparation protocols for mica surfaces. We profile thickness and refractive index of a nanometer-thin liquid film at high resolution with a newly developed three-dimensional scanning technique in the extended surface forces apparatus. We propose that the recently reported density anomalies in the thin liquid film are intimately coupled to the presence of local surface nonparallelism and nanoparticles that are produced during a widely used mica-cutting procedure. Measurements of cyclohexane confined between near parallel, nanoparticle-free mica surfaces contrast markedly with those reported in earlier studies.