The acquisition of dense 3D data sets is of great importance, but also a challenge for scanning probe microscopy (SPM). Thermal drift often induces severe distortions in the data, which usually constrains the acquisition of dense data sets to experiments under ultra-high vacuum and low-temperature conditions. Atom tracking is an elegant approach to compensate for thermal drift and to position the microscope tip with highest precision. Here, we present a flexible drift compensation system which can easily be connected to existing SPM hardware. Furthermore, we describe a 3D data acquisition and position correction protocol, which is capable of handling large and non-linear drift as typically present in room temperature measurements. This protocol is based on atom-tracking for precise positioning of the tip and we are able to acquire dense 3D data sets over several hours at room temperature. The performance of the protocol is demonstrated by presenting 3D data taken on a CaCO(3)(10 ̅14) surface with the data density being as large as 85×85×500 pixel.