The invention comprises an apparatus 10 and a method 100 for purifying biomolecules 28. Magnetizable particles 35 and a group of magnetizable pins 40 are used for binding biomolecules 28 to the magnetizable particles 35 using a binding buffer 30b, and for transferring the magnetizable particles 35 forming a particle-biomolecule complex 36. The apparatus 10 comprises an incubation unit 60 that allows for an upscaling of a maximum volume of a sample material. Furthermore the apparatus 10 comprises counter magnets 50 which are arranged on cavities 20. Solutions 30 comprising the biomolecules 28 and the magnetizable particles 35 are disposed in the cavities. The use of counter magnets 50 improves the quality of an eluate. Furthermore the invention comprises a system 800 and a method 900 for a diagnostically purifying of biomolecules 28. The method 900 further comprises a controlling of method steps and a selection of substances and reagents (for example the magnetizable particles 35) based on information automatically collected from, for example, the samples and/or derived from used substances and reagents. The system 800 fulfills requirements of medical diagnostics.