Systems for performing a medical procedure and associated methods and devices are disclosed herein. In some embodiments, a system for performing a medical procedure includes an elongate flexible device configured to be introduced into an anatomic cavity of a patient, and a sensor system carried by the elongate flexible device and configured to obtain location data of the anatomic structure. The system can be configured to perform operations comprising: generating a 3D anatomic model based on first location data, the 3D anatomic model including an object within the anatomic cavity, based on second location data of the elongate flexible device when the object is within the image, and providing guidance for deploying an access tool along an access path through a patient's skin to the object based, at least in part, on the 3D anatomic model.