We investigate the effect of process-induced damage (PID) caused by reactive ion etching using methanol (Me-OH) gas on the magnetic properties of the CoFeB free layer in a magnetic tunnel junction with a perpendicular easy axis (p-MTJ), and on the tunnel magnetoresistance (TMR) ratio of CoFeB-MgO p-MTJs. The dot pattern of the MTJ stack with size varied from 65 to 430nm etched by the Me-OH plasma showed a smaller coercivity (Hc) than that fabricated by Ar ion milling. The increase in Hc was observed in the dot pattern of large size (430nm) upon increasing He/H2 plasma treatment temperature after the Me-OH etching. A possible origin of the increase in Hc is the increase in nucleation field after He/H2 treatment. This suggests that Hc of the large dot pattern has the potential to be an index for detecting PID during the MTJ fabrication process. The TMR ratio of CoFeB-MgO p-MTJ deteriorated after the Me-OH plasma etching. This PID was considered to be due to oxidation from the pattern edge of the CoFeB free layer of the MTJ. The recovery process by the He/H2 plasma treatment was examined just after the Me-OH etching to reduce the oxidized part. The median TMR ratio of 102%, which is 5% higher than that of the sample without the He/H2 treatment, was observed after applying this reductive treatment at 180 °C. In addition, the recovery process had scalability with MTJ size, as the effect was observed more clearly in the MTJ smaller than 97 nm.