A method and clamp system for use on an ion implanter system for aligning a cathode and filament relative to one another in-situ are disclosed. The invention includes a clamp system having a clamp including a first clamp member separably coupled to a second clamp member, and an opening to a mount portion of one of the cathode and the filament in at least one of the clamp members. Each clamp member includes a surface to engage a mount portion of one of the cathode and the filament. The opening is adapted to receive a positioning tool to position the cathode and the filament relative to one another by moving the mount portion when the clamp is released. The mount portion may include a tool receiving member to facilitate accurate positioning.