We have developed a novel platform for selective binding of magnetic labels on planar Hall resistance sensor (PHR) for biosensing applications. The photoresist (PR) micro wells were prepared on the PHR sensor junctions to trap the magnetic bead at specified locations on the sensor surface and thin layer of Au was sputtered in the PR wells immobilize bimolecular. The Au surface is functionalized with single-stranded oligonucleotide and further biotin was used to immobilize streptavidin coated magnetic labels (Dynabeads Myone 1.0 microm, Invitrogen Co.). After removal of the PR wells on the sensor surface the non specific binding magnetic labels were successfully removed and only the chemically bounded magnetic labels were remained on the Au surface for detection of biomolecules using PHR sensor. We controlled the number of magnetic labels on the PHR sensor surface by using different sizes of the PR well on the junctions. The specifically bounded magnetic labels were successfully detected by characterizing the individual PHR sensor junctions. This technique enables the complete control over the magnetic labels for selective binding of biomolecules on the sensor surface for increasing the sensitivity of the PHR sensor as well as removal of the non specific bindings on the sensor surface.