You still show no code (i.e., no effort), so I probably shouldn't respond in this way. Please try to make a greater effort in future.

This uses the  \K regex operator, available with Perl versions 5.10 and above. (Update: You should state the Perl version you're working with.) The  dd (from Data::Dump) statement at the end shows that the contents of the  @lines array have been changed "in place" (the  $line scalar is aliased to each element of the array).

c:\@Work\Perl\monks>perl -wMstrict -le
"use 5.010;
 ;;
 use Data::Dump;
 ;;
 my @lines = (
   'X c:\temp\onefilename.txt with time =10day2h::56m::25s',
   'Y c:\temp\secondfilename.txt with time =5day3h::46m::45s',
   );
 ;;
 for my $line (@lines) {
   print qq{'$line'};
   $line =~ s{ \G (?: [[:upper:]] \K \s+ | \S+ \K \s+ \D+ | \d+ \K \D+
+) }
             {,}xmsg;
   print qq{'$line' \n};
   }
 ;;
 dd \@lines;
"
'X c:\temp\onefilename.txt with time =10day2h::56m::25s'
'X,c:\temp\onefilename.txt,10,2,56,25,'

'Y c:\temp\secondfilename.txt with time =5day3h::46m::45s'
'Y,c:\temp\secondfilename.txt,5,3,46,45,'

[
  "X,c:\\temp\\onefilename.txt,10,2,56,25,",
  "Y,c:\\temp\\secondfilename.txt,5,3,46,45,",
]
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Please see perlre, perlrequick, and especially perlretut.