The Allan variance (AVAR) is widely used to measure the stability of experimental time series. Specifically, the AVAR is commonly used in space applications, such as for monitoring the clocks of the Global Navigation Satellite Systems (GNSSs). In these applications the experimental data present some peculiar aspects which are not generally encountered when the measurements are carried out in a laboratory. Space clocks data can in fact present outliers, jumps and missing values which corrupt the clock characterization. Therefore, an efficient preprocessing is fundamental to ensure a proper data analysis and to improve the stability estimation performed with the AVAR or other similar variances. In this work we propose a preprocessing algorithm and its implementation in a robust software code (in MATLAB® language) able to deal with time series of experimental data affected by nonstationarities and missing data; our method is properly detecting and removing anomalous behaviors, hence making the subsequent stability analysis more reliable.