A numerical model is proposed to simulate the isotropic wet etching of silicon through an aperture of a mask to produce microlenses molds. The etching process is based on aqueous solutions of HF and HNO3 in the range of concentrations where etching rate depends mostly on mass-transfer effects. In the considered case the etching rate is defined by diffusion of F− ions to the (oxidized) silicon surface. The simulation is built with the finite element method (FEM) coupled with the level set method (LSM). Our model does not assume an infinite reaction rate on the etched surface. We investigate the influence of finite rate of the reaction on the shape of the etched structures. We investigate 2D and axis-symmetric geometrical cases, properly suited for microlenses fabrication applications. The fitting of the model parameters with experimental data is thus presented. A simplified method to simulate chaotic stirring of the etchant mixture is also proposed to study common experimental setups where the etching baker is agitated. The etching of prefabricated silicon structures is analysed in order to add the possibility of more flexible design of the fabricated structures.