The paper discusses some aspects of an ongoing project aimed at the development of a methodology and proper software tools for building and usage of academic digital libraries. A particular functional model of academic digital library has been proposed and analyzed. The emphasis falls on some solutions of the large set of problems concerning the development of adequate mechanisms for semantics oriented search in multilingual digital libraries. An ontology-based approach is suggested in order to standardize the semantic annotation of the library resources and to facilitate the implementation of the functionality of the search engine. The main features of a prototype of knowledge-based search engine for a multilingual academic digital library with research and learning materials are discussed. This search engine uses proper ontologies describing the conceptual knowledge considerable for the chosen domains and in this way it is capable of retrieving and filtering documents by their semantic properties.