Here is one way:

use strict;

# look ma! no $_! ;)

while (<DATA>) {
   s/\d\d(\d\d)\.(\d+)/$1$2/;
   print;
}

__DATA__
1996.40637
1996.41064
1996.41199
1996.41467
1996.41882
[download]

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UPDATE: ack! i see it now: you want =~, not = for your substitution lines.

Here is my above while loop with the implicit $_:

while ($_ = <DATA>) {
   $_ =~ s/\d\d(\d\d)\.(\d+)/$1$2/;
   print $_;
}
[download]

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UPDATE 2: re japhy
DOH! ;)

jeffa