Well, stat() gives you epoch seconds since last modification. Then you'll need to get the epoch seconds for 12:00 am on the present date -- use localtime() to get the day, month, and year, then pass those back to timelocal() with hours, minutes, and seconds set to zero to get the time of midnight. Now any file for which the stat() time is greater than the time of midnight was made today.

use Time::Local;
my $mtime=(stat("filename.extension"))[13];
my ($day, $month, $year)=(localtime())[3,4,5];
my $midnight=timelocal(0,0,0,$day,$month,$year);
unlink ("filename.extension") if ($mtime>$midnight);
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