Automatic data extraction from medical legacy systems into archetype-based systems is analyzed, developed and tested in this work. Electronic health record system (EHRS) is a must in today’s healthcare environment. Lots of up-to-date medical systems are still built with classic development approaches, with semantics hard coded into systems. Modern EHRS standards propose new “two-level” methodology, which is based on separation of knowledge and information levels. This work suggests a methodology for heterogenic medical legacy systems that exist today to be transformed into ones, built with “two-level” methodology. Transformation is based on knowledge, residing in new system. By creating a comprehensive transformation scheme, it is possible to analyze and extract relevant data from semi structured or unstructured text fields with mixed information. Suggested methodology is tested with software prototype by extracting laboratory results of clinical blood test from semi structured fields of cardiology database. Achieved results are about 95% of data successfully transferred from legacy system. This approach preserves medical data accumulated during long years of work and transforms it into more useful form, creating structured data from unstructured text fields. It allows an automatic means of information technologies to be used by medicine expert to analyze and interpret legacy data (draw charts, calculate statistics and so on).