Fluorescent in situ hybridization (FISH) assays to detect gene amplification such as HER2 or MET in tumors are used for prognosis evaluation and selection of targeted therapies. Although FISH guidelines recommended 4~6 μm FFPE sections, many laboratories use 2~3 μm sections, which is a common practice for H&E staining and immunohistochemistry. A former study concluded that section thickness did not affect FISH results. We found, however, that thinner FFPE sections may lead to false negative results for gene amplification. A mathematic model was constructed and cell-line based controls with known gene copy number were prepared, and the model had a reasonable fit with the experimental data. The model revealed that even when counting the apparently full-sized nuclear images, many of them have partial volumes, which leads to under-estimation of gene copy number. Therefore, improperly thinner sections are prone to give false negative results, and thicker sections give a better approximation to the true value. The discrepancy between this and the former study was discussed. In summary, the model applies generally to FISH/ISH detection of gene copy number, and section thickness is an important parameter to control for precision medicine research, assay development, clinical trials and daily practice in pathology laboratory.