Use pipe "|" instead of ">" to pass data from one program to another:

type * | perl -ne "print unless /^Total\s\d{1,5}/" > ..\newFile
[download]

Using only Perl:

perl -e "while (<*>) {open(F,$_) or next;while(<F>){print unless /^Tot
+al\s\d{1,5}/}}" > ..\newFile
[download]

Note: this code has errors, but works as an example.