The "TNOs are Cool!: A survey of the trans-Neptunian region" is a Herschel Open Time Key Program that aims to characterize planetary bodies at the outskirts of the Solar System using PACS and SPIRE data, mostly taken as scan-maps. In this paper we summarize our PACS data reduction scheme that uses a modified version of the standard pipeline for basic data reduction, optimized for faint, moving targets. Due to the low flux density of our targets the observations are confusion noise limited or at least often affected by bright nearby background sources at 100 and 160\,$μ$m. To overcome these problems we developed techniques to characterize and eliminate the background at the positions of our targets and a background matching technique to compensate for pointing errors. We derive a variety of maps as science data products that are used depending on the source flux and background levels and the scientific purpose. Our techniques are also applicable to a wealth of other Herschel solar system photometric observations, e.g. comets and near-Earth asteroids. The principles of our observing strategies and reduction techniques for moving targets will also be applicable for similar surveys of future infrared space projects. ; Comment: Accepted for publication in Experimental Astronomy