Nanoparticle image velocimetry (nano-PIV), based on total internal reflection fluorescent microscopy, is very useful to investigate fluid flows within approximately 100 nm from a surface; but so far it has only been applied to flow over smooth surfaces. Here we show that it can also be applied to flow over a topologically structured surface, provided that the surface structures can be carefully configured not to disrupt the evanescent-wave illumination. We apply nano-PIV to quantify the flow velocity distribution over a polydimethylsiloxane surface, with a periodic gratinglike structure (with 215 nm height and 2 mum period) fabricated using our customized multilevel lithography method. The measured tracer displacement data are in good agreement with the computed theoretical values. These results demonstrate new possibilities to study the interactions between fluid flow and topologically structured surfaces.