Another way, using decorate-undecorate, and including the latest requirement for case-insensitive sorting (but see also Sort::Maker):

>perl -wMstrict -le
"my $ar = [
   qw(X1 Mt10 mT2 y20 Y1 Y10 mt20 x20 X10)
   ];
 ;;
 my @sorted =
   map { undecorate($_) }
   sort
   map { print qq{'$_'};  $_ }
   map { decorate($_) }
   @$ar
   ;
 ;;
 print qq{'$_'} for @sorted;
 ;;
 use constant WIDTH => 10;
 use constant SEP   => ':';
 ;;
 sub decorate {
   my ($num)   = $_[0] =~ m{ (\d+)          }xms;
   my ($alpha) = $_[0] =~ m{ ([[:alpha:]]+) }xms;
   return sprintf '%0*d%s%s%s', WIDTH, $num, lc($alpha), SEP, $_[0];
   }
 ;;
 sub undecorate {
   return substr $_[0], 1 + index $_[0], SEP;
   }
"
'0000000001x:X1'
'0000000010mt:Mt10'
'0000000002mt:mT2'
'0000000020y:y20'
'0000000001y:Y1'
'0000000010y:Y10'
'0000000020mt:mt20'
'0000000020x:x20'
'0000000010x:X10'
'X1'
'Y1'
'mT2'
'Mt10'
'X10'
'Y10'
'mt20'
'x20'
'y20'
[download]

Note: The  map { print qq{'$_'};  $_ } step above is just to show the effect of decoration.

Also: The two regexes could be combined into one in the  decorate() function.

Update: See also Re: Help Manipulating Sort with Subroutines for another variation of this 'pattern'.