Controlled navigation of swimming micro robots inside fluid filled channels is necessary for applications in living tissues and vessels. Hydrodynamic behavior inside channels and interaction with channel walls need to be understood well for successful design and control of these surgical-tools-to-be. In this study, two different mechanisms are used for forward and lateral motion: rotation of helices in the direction of the helical axis leads to forward motion in the viscous fluid, and rolling due to wall traction results with the lateral motion near the wall. Experiments are conducted using a magnetic helical swimmer having 1.5 mm in length and 0.5 mm in diameter placed inside two different glycerol-filled channels with rectangular cross sections. The strength, direction and rotational frequency of the externally applied rotating magnetic field are used as inputs to control the position and direction of the micro swimmer in Y- and T-shaped channels.