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perl -pe 's/\bME_//g' FILEA > FILEB

Note sed -r is GNU sed. With it, you could also do this:
sed 's/\<ME_//g' file

Try using EREs (extended regexes):sed -r 's/(^|,| )ME\_/\1/g' file3
ABC_X,DME_X, FCX_X