Two-photon lithography (TPL) is a polymerization-based direct laser writing process that is capable of fabricating arbitrarily complex three-dimensional (3D) structures with submicron features. Traditional TPL techniques have limited scalability due to the slow point-by-point serial writing scheme. The femtosecond projection TPL (FP-TPL) technique increases printing rate by a thousand times by enabling layer-by-layer parallelization. However, parallelization alters the time and the length scales of the underlying polymerization process. It is therefore challenging to apply the models of serial TPL to accurately predict process outcome during FP-TPL. To solve this problem, we have generated a finite element model of the polymerization process on the time and length scales relevant to FP-TPL. The model is based on the reaction-diffusion mechanism that underlies polymerization. We have applied this model to predict the geometry of nanowires printed under a variety of conditions and compared these predictions against empirical data. Our model accurately predicts the nanowire widths. However, accuracy of aspect ratio prediction is hindered by uncertain values of the chemical properties of the photopolymer. Nevertheless, our results demonstrate that the reaction-diffusion model can accurately capture the effect of controllable parameters on FP-TPL process outcome and can therefore be used for process control and optimization.