undef will work just fine on the de-refd ref passed to the sub-routine:

use strict;
use warnings;
use Data::Dumper;

sub undef_ref
{    
    my $ref = shift;
    my @struct = @$ref;
    undef @$ref; ## Blow away original
    print '='x20;
    print"\nStruct is\n";
    print Dumper(@struct),"\nIn undef_ref\n";
}

my @struct = ('a','b','c','d','e');
undef_ref(\@struct);
print '='x20;
print"\n";
print "Struct is\n",Dumper(@struct),"\nOutside undef_ref\n";
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The perlreftut & perlref pages in the core documentation is a great place to start.