The application of electrical fields within a microfluidic channel enables many forms of manipulation necessary for lab-on-a-chip devices. Patterning electrodes inside the microfluidic channel generally requires multi-step optical lithography. Here, we utilize an ion-implantation process to pattern 3D electrodes within a fluidic channel made of polydimethylsiloxane (PDMS). Electrode structuring within the channel is achieved by ion implantation at a 40° angle with a metal shadow mask. The advantages of three-dimensional structuring of electrodes within a fluidic channel over traditional planar electrode designs are discussed. Two possible applications are presented: asymmetric particles can be aligned in any of the three axial dimensions with electro-orientation; colloidal focusing and concentration within a fluidic channel can be achieved through dielectrophoresis. Demonstrations are shown with E. coli, a rod shaped bacteria, and indicate the potential that ion-implanted microfluidic channels have for manipulations in the context of lab-on-a-chip devices.