Resistive pulse sensors (RPS) are based on the detection principle of partial and non-permanent obstruction of an electrically conducting channel. The integration of RPS in microfluidics has the potential for detections at the molecular level. Current challenges involve limitations in fabrication technology, most notably the finite structure accuracy and fabrication repeatability, which have a direct and strong impact on RPS device performance. In this work, we analyzed the geometrical structure and performance of a nanofabricated RPS device and iteratively used the experimental data to propose an adequate numerical model which also accounts for fabrication imperfections beyond the optical resolution limit. The proposed model for a nano-RPS was validated and able to augment the understating of the structure and operation of a microdevice.Clinical Relevance- This work is part of a greater effort to bring microfluidics devices closer to patients for bedside analysis of blood, or other human fluids, for instance. These devices can potentially perform screening for multiple targets in one sample. New devices often need to go through design, prototyping and bench tests, simulation models as the one presented can increase the chances of the device to get to the market in reduced time.