In vivo, the tissue environment often strongly confines cells and multicellular assemblies, especially in cancer. Therefore, replicating these confined environments in situ is crucial for studying their effects on cellular systems. We used two-photon lithography to print directly within and near multicellular assemblies. For instance, we created dome-shaped confinements with micrometer-sized openings to enclose cancer spheroids. This allowed us to examine the migration behavior of cancer cells and the effects of confinement on the spheroid. We found that confinement reduced cell migration speed and impacted actin dynamics. Additionally, two-photon lithography offers a new way to analyze specific regions of multicellular structures by enabling in situ separation from a spheroid. This is possible because the printing laser can penetrate the nearly transparent multicellular structure. In addition, also elastic structures to mechanically stimulate cells can be used for the in situ control of cells. Hence, two-photon lithography is effective for controlling the growth, migration, and morphology of live cells, making it highly relevant for studying cell responses to changes in their physical microenvironment.