To strip the periods, use a regex like s/\.//g;. Then save the file. Then open the file with DBD::CSV and use this kind of approach to create a new file that only has the columns you want:

# my $dbh = DBI->connect( ... );
my $wanted_cols = join ',',qw( colname1 colname2 ...);
$dbh->do("
    CREATE TABLE new_table
        AS SELECT ($wanted_cols) FROM old_table
");
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That will make a new CSV file that is an exact duplicate of the original except leaving out the columns you don't want. The "CREATE TABLE AS SELECT ..." syntax is only available in the newest version of SQL::Statement (the SQL engine for DBD::CSV).