Glioblastoma multiforme (GBM) is one of the most aggressive brain tumors. The majority of modern treatment methods for GBM are not sufficiently effective with a median survival varying from 9 to 14 months. One of the main reasons for the therapeutic resistance of GBM is attributed to cancer stem cells. Pharmaceuticals that can effectively eliminate cancer stem cells do not exist. Experimentally, we have shown that cancer stem cells can be specifically affected to arrest adhesion, proliferation and migration, and other key functions. The main target of this therapy involves membrane intracellular signaling pathways of cancer stem cells that are not subject to neoplastic transformation. An effect on such a complex target requires the development of innovative biotechnological approaches. The research analysis of modern approaches towards creating biomedical drugs for treating cancer stem cells of glioblastoma multiforme is based on advances in the latest cellular and post-genomic technologies. The combination of targeted therapy with regulation of the key functions of cancer stem cells using cell systems with a remodeled proteome is suggested.