Abstract: A method of and system for pretreating the lumen of a catheter or small diameter tubing. A vacuum chamber includes a microwave port and a microwave supply subsystem including a microwave generator, and a circular polarizer produces circularly polarized microwaves propagated into the vacuum chamber via the port at a frequency which produces electron cyclotron resonance. A magnetic coil about the vacuum chamber generates a magnetic field in the vacuum chamber with magnetic field lines co-linear with the propagation direction of the microwaves. A catheter manifold positions at least one catheter in the vacuum chamber and supplies a gas within the catheter lumen to generate a plasma in the lumen for pretreating the same.