A method and device for separating from samples magnetic particles that contain capture compounds on their surfaces. The device includes a sheath including a magnet and including orienting pin adapted to concentrate or direct a magnetic field of the magnet; and a magnetizable plate with lid holes for receiving a vessel lid of a vessel, the magnetizable plate configured to receive the sheath and position the orienting pin over the vessel lid. In one method, magnetic beads with attached molecules are collected in the lids of the reaction vessel by the magnetic separator device provided herein and the separated magnetic particles, which carry the molecules of interest through affinity-based attachment chemistry and are held in the lid by the magnet of the device, are released into a new vessel containing a solution by removal of the separator device without the need for pipettes or liquid handling devices.