Perhaps you could do this in a couple of stages. In stage one, read all of the input files, and build up a database with a column for "trap sender" and a column for the logfile entry, each row in the DB representing an entry from one of the input logfiles. It takes only one database connection to build up the database.

Then in the second pass, prepare a query such as "SELECT logentry FROM sometable WHERE trap_sender=?". Then one by one open a file for a particular user, execute the query with that user's name, and spill to that user's logfile the entries returned by fetchrow.

That way, you never have to hold all 100mb in memory at once, you never have to hold hundreds of open filehandles, you don't have to suffer the poor performance of opening and closing filehandles hundreds of times over and over again, and you get some practice with DBI. DBD::SQLite would be a great lightweight database on which to build the implementation of this strategy.