The Mission Support System (MSS) is an open source software package that has been used for planning flight tracks of scientific aircraft in multiple measurement campaigns during the last decade. Here, we describe the MSS software and its use during the SouthTRAC measurement campaign in 2019. As an example for how the MSS software is used in conjunction with many datasets, we describe the planning of a single flight probing orographic gravity waves propagating up into the lower mesosphere.