We present a method designed to efficiently extract optical signals from InGaAs avalanche photodiodes (APDs) operated in gated mode. In particular, our method permits an estimation of the fraction of counts that actually results from the signal being measured, as opposed to being produced by noise mechanisms, specifically by afterpulsing. Our method in principle allows the use of InGaAs APDs at high detection efficiencies, with the full operation bandwidth, either with or without resorting to the application of a dead-time. As we show below, our method can be used in configurations where afterpulsing exceeds the genuine signal by orders of magnitude, even near saturation. The algorithms that we have developed are suitable to be used either in real-time processing of raw detection probabilities or in post-processing applications, after a calibration step has been performed. The algorithms that we propose here can complement technologies designed for the reduction of afterpulsing.