Removing nanometer scale particles from patterned substrates is a critical, yet challenging, technical task with numerous applications. Due to environmental concerns, there is a drive to reduce chemical usage and waste in semiconductor and other nano-technology industries. The laser plasma method is a novel removal method for nanoparticles. For the work reported in this study, the method is applied to substrates with features, i.e. trenches and pinholes. The technique, which is dry and non-contact, takes advantage of shock wavefronts initiated by plasma formation under a focused laser beam pulse and their interaction with the substrate. In the reported experiments, a Q-switched Nd : YAG pulsed laser is employed as a plasma and shockwave generation source. Various mechanisms are responsible for the removal effect. The strong shock wave in air generates complex pressure wavefields resulting in both drag and lift on the particle and acceleration of the substrate. However, shock waves are not transmitted into the solid substrate as discontinuous shock fronts due to a large difference between the relevant wave phase speeds in the two media. Also, damage concerns due to cavitation, which is a common effect in megasonic cleaning, are avoided. However, damage due to the high temperatures associated with the plasma formation is found to be an issue. Patterned silicon wafers and micrometer level pinholes were used for the particle removal experiments. The effects of the distance between the surface and the plasma boundary on the removal efficiency are reported. With this method, we were able to remove particles from the wall of a micrometer level pinhole and patterned silicon wafers.