If your files are not very big you can solve the problem with:

print F2 grep {/<EMP>/} <F1> ;
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This will upload F1, and "grep" all the lines that contain "<EMP>"

A more gentle solution (that doesn't upload F1 in memory):

while (<F1>){
  #Some conversions here
  print F2 if /<EMP>/;
}
[download]

Hope this helps!

citromatik

PD: Your code seems to be valid. check if you are opening F2 correctly and try removing it before running the script again