In this paper, we present experimental and numerical studies on the microstructures of a cholesteric liquid crystal (CLC) confined in rectangular micron-channels. By using a sequence of microfabrication techniques we fabricated the micro-sized channels with accurately controlled size, aspect ratio and homeotropic surface anchoring. Through optical microscopic studies we established a phase diagram for the liquid crystal defect textures as a function of the channel depth and width. For the channel width larger than ∼2 times the cholesteric pitch p, the LC molecules are oriented primarily vertical to the channel when the channel depth is below 0.75p, form bubble domain defects when the channel depth is around 0.75p, and form stripe textures when the cell depth is above the cholesteric pitch p. In addition, the bubble domain size and the stripe texture periodicity are found to grow with the increase of the channel width. For the channel width smaller than ∼2p and the channel depth between 0.6p to 1.1p, no textures can be observed in the channels. Numerical simulations based on a director tensor relaxation approach yield detailed molecular director fields, and show that the bubble domain defects are baby-skyrmions and that the stripes are the first type of cholesteric fingerprints. A comparison with previous experiments and numerical simulations indicates that the size of the microchannels also influences what type of soliton-like topological textures form in the CLCs confined in the channels.