In the age, when empirical sciences, such as cognitive psychology, artificial intelligence and neuro-ethics, go on invading the territory remained with philosophy after the Kantian ‘Copernican revolution’, the inevitable question is posed: is philosophy as such becoming only an item in the mankind's historical archive and a portion of an educated person's background, while having no more impact on the actual search for truth? In the paper, through a partial revision of the conventional views on the structure of scientific knowledge, the legitimate application area for philosophers' professional competences is determined. First, arguments are presented that demonstrate that possible claims of philosophy to be a science-independent description of the world are inappropriate. Then, the analysis of scientific knowledge structure reveals the previously largely ignored element therein: namely, scientific ontologies or conceptual schemes. A principal point is logical independence of scientific ontologies from the theoretical and empirical components of science. A choice of an ontology is considered here to be a free choice and a creative act of a scientist that affects competitive advantages of a proposed theory. The analysis and criticism of scientific ontologies is proposed to be regarded as a legitimate application area of philosophical competences, along with metatology, which is a normative discipline interpreting opportunities and rules for constructing subject ontologies.