Connectome Mapper 3 (CMP3) is an open-source processing pipeline software, written in Python 3, for multi-scale multi-modal connectome mapping of the human brain. It provides researchers with a unique workflow, implemented in accordance with the Brain Imaging Data Structure (BIDS) App framework (Gorgolewski et al., 2017), that leverages a number of widely adopted software tools to map a graph representation of the structural and functional connections between brain regions, the connectome, at multiple scales. The workflow can take any structural / diffusion / resting-state functional Magnetic Resonance Imaging (MRI) dataset structured according to the BIDS standard (Gorgolewski et al., 2016), and is intended to be run via its Docker and Singularity/Apptainer containerized versions. To improve its accessibility, CMP3 comes with a graphical user interface, which supports the user in all the steps involved in the configuration of the pipelines, the configuration and execution of the BIDS App, and the control of the output quality. CMP3 has been successfully employed in a number of research papers, and is currently being extended to electroencephalography, to offer a solid multi-modal framework to the community for the investigation of brain network function and organization at specific scales, as well as a map that links different spatial and temporal scales. CMP3 is available from the Python Package Index (PyPI), and the container images are available from DockerHub and Sylabs Cloud.