We have applied the atomic force microscopy (AFM) lithography technique to electrically phase-separated (La,Pr,Ca)MnO3 (LPCMO) thin films. It was found that the maximum pattern height of 10.5 nm for the as-deposited film was much higher than that of 5.3 nm for the annealed film, suggesting that AFM lithography of LPCMO thin film was highly influenced by oxygen nonstoichiometry that enhances ion migration. The nanochannel with 150 nm width was fabricated using this technique. The nanostructure shows insulating behavior under H=0 T and large hysteretic behavior accompanied with metal-insulator transition temperature Tp=140 and 170 K upon cooling and warming under 5 T. In contrast, the unpatterned film has Tp=170 K (H=0 T) and 240 K (H=5 T) without large hysteretic behavior. The difference between the nanochannel and the unpatterned film can be related to the electronic phase separation.