We experimentally report the geometric effect on photonic nanojet generated by dielectric microcylinders with non-cylindrical cross-sections. The non-cylindrical cross-sections include truncated microcylinders and elliptical microcylinders. The truncated microcylinder is formed with the cutting thickness. The elliptical microcylinder is defined by ratio of minor to major axes. The specific spatial electromagnetic fields for microcylinders with different non-cylindrical cross-sections are studied by using finite-difference time-domain calculation. The direct imaging of photonic nanojets for microcylinders with different non-cylindrical cross-sections are performed with a scanning optical microscope system. The field distribution and location of photonic nanojet depending on the various spatial shapes are experimentally demonstrated. The photonic nanojet with long focal length and low divergence could be used to scan over a target to obtain a large area image when the non-cylindrical micro-media are coupled with a conventional optical microscope.