Estimating the gain of an antenna prototype is an important step during both design and validation phases. Nevertheless, many small technology companies and universities are not provided with adequate infrastructure to run this type of test. In this paper, we propose a computational tool to deal with undesirable contributions coming from non-ideal test conditions over electromagnetic measurements. It is based on auto-tunable filters and therefore it allows a lab technician to run the test without a major knowledge on signal processing. After a series of evaluations based on lab measurements, the proposed tool gives results as good as those provided by two other approaches but with a reduction of the total number of experimental runs. Furthermore, it is more efficient than the traditional time gating approach for low signal-to-noise ratio environments. Finally, a validation with different antennas and test sites confirmes its robustness.