The measurements of HCl and CH4 atmospheric total abundance is very important, because these minor gases play a fundamental role in the stratospheric ozone cycle and in the climatic change. In fact, the first is considered source and sink for chlorine compounds; the latter is a greenhouse gas (26%) and can contribute to the hydrochloric acid formation. HCl and CH4 present a vibrorotational absorption spectrum in the near infrared (3-4 micron). For this reason it is possible to use a Fabry-Perot interferometer (FPI) as a multiple narrow band filter with an appropriate free spectral range (FSR), so its transmission bands overlap the absorption lines of gas under observation. A remote sensor called NISES (Near Infrared Single-Etalon Sensor) and based on a plane FPI with a dynamic control of the etalon gap, is developing. It utilizes the direct sun radiation collected by a solar tracker to detect atmospheric HCl and CH4 slant columns and its suitable for both ground based and airborne applications. The model MAES (Mathematical Algorithm for Etalon Sensor) has been used to study the main optical characteristics of the FPI (free spectral range, finesse, transmission lines number) and to optimize the instrumental response over a wide range of atmospheric conditions. Moreover, line by line computations of atmospheric layer optical depths and radiances are performed, using HARTCODE (R. Rizzi et al. submitted to Applied optics), so a sequence of different Free spectral Range (FSRs), during the measurements itself, is proposed to minimize the water vapor and gases interfering contribution. The main optical characteristics of an FPI and its deployment for atmospheric sensing are discussed; the result of model simulation and the layout of the HCl sensor are presented as well as some preliminary tests.