While controlling particle diffusion in a confined geometry is a popular approach taken by both natural and artificial systems, it has not been widely adopted for controlling light transport in random media, where wave interference effects play a critical role. The transmission eigenchannels determine not only light propagation through the disordered system but also the energy concentrated inside. Here, we propose and demonstrate an effective approach to modify these channels, whose structures are considered to be universal in conventional diffusive waveguides. By adjusting the waveguide geometry, we are able to alter the spatial profiles of the transmission eigenchannels significantly and deterministically from the universal ones. In addition, evanescent channels may be converted to propagating channels by gradually increasing the waveguide cross-section. Our approach allows to control not only the transmitted and reflected light, but also the depth profile of energy density inside the scattering system. In particular geometries, perfect reflection channels are created, and their large penetration depth into the turbid medium as well as the complete return of probe light to the input end would greatly benefit sensing and imaging applications. Absorption along with geometry can be further employed for tuning the decay length of energy flux inside the random system, which cannot be achieved in a common waveguide with uniform cross-section. Our approach relies solely on confined geometry and does not require any modification of intrinsic disorder, thus it is applicable to a variety of systems and also to other types of waves.