Nanowires of two-dimensional (2D) crystals of type-II superconductor NbSe$_2$ prepared by electron-beam lithography were studied, focusing on the effect of the motion of Abrikosov vortices. We present magnetoresistance measurements on these nanowires and show features related to vortex crossing, trapping, and pinning. The vortex crossing rate was found to vary non-monotonically with the applied field, which results in non-monotonic magnetoresistance variations in agreement with theoretical calculations in the London approximation. Above the lower critical field, $H_{c1}$, the crossing rate is also influenced by vortices trapped by sample boundaries or pinning centers, leading to sample-specific magnetoresistance patterns. We show that the local pinning potential can be modified by intentionally introducing surface adsorbates, making the magnetoresistance pattern a magneto fingerprint of the sample-specific configuration of vortex pinning centers in a 2D crystal superconducting nanowire.
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