We demonstrate that 2D distributions of non-spherical near-coalescence silver nanoparticles (NPs) embedded in an ultrathin dielectric film can be reorganized, shaped and aligned by exposure to ultrashort laser pulses. As-grown samples prepared by pulsed laser deposition show a broad absorption band with a surface plasmon resonance (SPR) at 650 nm, which can be blue-shifted down to 440 nm and transformed to show polarization anisotropy. In situ white light probing of the spectral sample transmission allows control during irradiation of the position and polarization anisotropy of the SPR, effectively controlling particle reorganization and shaping. Using the high spatial resolution of the optical probe technique (better than 10 μm), the dependence of the nanoparticle shape and distribution on the local fluence can be studied in a single irradiated region. The results inferred from the spectral measurements have been confirmed by TEM studies, showing the formation of nanoparticles with prolate shape, preferential alignment along the polarization axis of the laser and a narrow size distribution. This simple and efficient approach for NP shaping and the straightforward extension to multilayer systems offer excellent perspectives for optical encoding, multidimensional data storage and fabrication of complex, polarization-sensitive spectral masks starting from thin films with near-coalescence distributions of NPs.