Cell culture techniques have evolved in the last decades and allow now testing anti-cancer drugs using tumor-like spheroids. We describe here issues and trouble-shooting solutions when generating spheroids from three human melanoma cell lines (A375, WM115 and WM266). A375 cells generated irregular shape spheroids that were difficult to study due to their fragility. Spheroids generated from all cell lines initially reduced their diameter and increased compacity before increasing in size overtime. Cells present at the periphery of the spheroids showed higher metabolic activity than cells present in the core of the spheroids. When grown as spheroids, a smaller fraction of the A375 and WM115 cells was sensitive to the chemotherapeutic agent temozolomide as compared to cells grown on flat surface. However, this difference was not observed with WM266 cells. Although the presence of spheroids resulted in a smaller fraction of WM155 cells sensitive to the anti-cancer agent vemurafenib, the opposite was observed with A375 cells. Among the cells, WM266 cells were the most resistant to vemurafenib. In conclusion, our study suggests that cell lines behave differently in terms of spheroid formation, and that the effect of the 3D cellular architecture on drug effect is cell type and drug dependent.