Some of the key challenges in the applications of graphene and carbon nanotubes are associated with their poor attachment to the substrate and poisoning of the catalyst by environmental contamination prior to the growth phase. Here we report a ‘protected catalyst’ technique which not only overcomes these challenges but also provides a new material production route compatible with many applications of carbon nanomaterials. The breakthrough technique involves capping the catalyst with a protective layer of a suitable material (examples include TiN, Cr, Ta) which protects the catalyst from environmental contaminants such as oxidation, etchant attack, etc., whilst maintaining carbon supply to the catalyst for the CVD growth of desired nanomaterial. A thin Fe catalyst layer remained protected due to the capping layer in the CF4 based reactive-ion-etching of SiO2. We show that the carbon nanostructures grown using this technique exhibit significantly improved adhesion to the substrate in sonication bath tests. We demonstrate the fabrication of 3D structures and CNT based vias in a buried catalyst arrangement using the protected catalyst technique. The technique also allows better control over various growth parameters such as number of graphene layers, growth rate, morphology, and structural quality.