The surface roughness of polymer thin films supported on nickel-coated silicon substrates was analyzed by angle-dependent total-reflection x-ray fluorescence (TXRF) in conjunction with atomic force microscopy (AFM). For highly rubbed polystyrene (PS) surfaces (500 cm rubbing length at a load of 2 g/cm(2) over a velour cloth) displaying sharp grooves and ridges, the TXRF showed no significant change while the AFM results revealed an anisotropic 6.08 nm root-mean-square roughness with an average peak-to-peak distance of 170 nm. These results were compared to the isotropic, gradually varying sinusoidal surface roughness of phase-separated polystyrene/poly(vinyl methyl ether) blend thin films. The AFM results were very similar to the results from the rubbed PS in terms of root-mean-square roughness and average peak-to-peak distance; however, the TXRF results revealed enhanced nickel fluorescence at incident angles smaller than the polymer critical angle for reflection. This discrepancy highlights some of the qualitative differences in surface topography between rubbed and phase-separated polymer thin films, and demonstrates the utility-of angle-dependent TXRF to study thin film roughness and planarity.