We report experimental measurements of the surface fluctuations of micron-thick oil films spread onto a solid substrate. We use a recently developed optical technique based on the measurement of the deflection of a laser beam triggered by changes in the local surface slope. When the liquid is spread on a flat substrate, fluctuation dynamics slow down as the thickness is decreased, in quantitative agreement with previous predictions. In addition, we investigate the consequences on surface fluctuations of the patterning of the substrate with a rectangular grating. For liquid film thicknesses smaller than the typical wavelength probed, we demonstrate that surface fluctuations are modified by the underlying pattern: The shape of the fluctuation spectra varies periodically with the spatial position over the pattern and, in addition, the fluctuations become locally anisotropic. However, the spatially averaged spectrum is isotropic.