qr{
     <%
        [^%]*
        %+
        (
           [^>%]
           [^%]*
           %+
        )*
     >
  }x;      

##</code><code>##

# Test Script
#Uncomment this next line for WAAAYYY too much info
#use re 'debug';


$cleanup=
qr{
     <%
        [^%]*
        %+
        (
           [^>%]
           [^%]*
           %+
        )*
     >
  }x;

@test= ( "stuff <% junk %> more stuff <% more junk %> end",
        "stuff <% junk% %> more stuff",
        "Go <% now %> to <% your %> home <% if %> you <% can %>",
        "<% %%>",
        "<%replace here%%>but not here%>",
        "1 <% xxx%%> 2 <%%> 3 <%>%> 4 <% >% %> 5 <%%%% xxx %%%%> 6 ",
        "<% %%> %>",
        "<%abcdefg>"x500,
        "<% %% %>");

foreach(@test)
{
  print "-"x60,$/,"Test: {$_}$/"; 
  s/$cleanup//g; 
  print "Result: {$_}$/";
}