The processing of vertical graphene nanowalls (VGNWs) via laser irradiation is proposed as a means to modulate their physicochemical properties. The effects of the number of applied pulses and fluence of each pulse are examined. Raman spectroscopy studies the effect of irradiation on the chemical structure of the VGNWs. Results show a decrease in density of defects and number of layers, which points toward a mechanism including evaporation of amorphous or loosely bonded C from defective points and recrystallization of graphene. Moreover, the effect of laser irradiation parameters on the morphology of Mo thin films deposited on VGNWs is investigated. The received thermal dosage results in the formation of particles. In this case, the number of pulses and pulse fluence are found to affect the size and distribution of these particles. The study provides a novel approach for the functionalization of VGNWs via laser irradiation, which can be extended to other graphene-based nanostructures.