3D genome organization is shaped by dynamic interactions with multiple structures in the nucleus, affecting gene expression outcomes. Technological breakthroughs have generated vast datasets reflecting various aspects of nuclear genome architecture in space and time. This paper is a step-by-step guide on how to generate publication-ready integrated 3D genome models from (raw) Hi-C data and from lamin-genome (LAD) contacts. (Paulsen and Collas, Methods Mol Biol. 2022;2301:337-352. doi: 10.1007/978-1-0716-1390-0_18).