See chomp for a way to do it.

I think you were looking for map not grep.

This

#!/usr/bin/perl -w

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

my @e1 = (
        '   bob',
        '    sue',
        '  joe_1',
);

my @e2 = (
        'bob',
        'sue',
        'joe1',
);

my @f = map { s/\W|_//g; $_ } @e1;

print Dumper(\@f);
print Dumper(\@e2);
[download]

Gives this output:

$VAR1 = [
          'bob',
          'sue',
          'joe1'
        ];
$VAR1 = [
          'bob',
          'sue',
          'joe1'
        ];
[download]

Also, it might be better to put more thought into your subject line next time. That helps other monks with a similar problem find this thread easier. For example, "remove spaces from array elements" might be good

Haven't tested it, but I believe that the code below will should strip out all of the "unwanted" characters in an array. ("Unwanted" as in non-alphanumeric, which is what I believe that you're asking for.)

foreach my $item (@array) {
  $item =~ s/\W//g; # Remove non-word characters
  $item =~ s/_//g; # Remove all underscores
}
[download]

grep{} is a filtering operation. It doesn't modify anything.
my @E = grep { !/^\n*$/ } @EuserADgrps;
means: transfer each item from @EuserADgrps to @E which satisfies the regex within the grep{}.

/^\n*$/ means: a string that may have zero or more \n characters, but no other characters - a pretty "rare duck"; perhaps a null string, "". When you negate that with the !, it means that for each item in @EuserADgrps, transfer it to @E if it is not one of these "rare ducks". I suspect that this grep{} does nothing to your actual data.

Use @X=map{..blah..;$_}@Y; to transform a Y into an X. But I don't think that you need that here either.

The chomp() function will remove trailing "new lines" from a string, or you can also use chomp() on an array. chomp(@x) will modify @x. So if you don't want that, make a copy:  @y=@x; chomp(@y);#See below:

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my @EuserADgrps = ("abc\n", "xyz\n");

my @E = grep { !/^\n*$/ } @EuserADgrps;  #so weird it's probably wrong

print Dumper \@EuserADgrps;
print Dumper \@E;

chomp(@EuserADgrps);           #this modifies the @EuserADgrps array
print "now after the chomp of ".'@EuserADgrps'." \n";
print Dumper \@EuserADgrps;

__END__
printout:
$VAR1 = [
          'abc
',
          'xyz
'
        ];
$VAR1 = [
          'abc
',
          'xyz
'
        ];
now after the chomp of @EuserADgrps 
$VAR1 = [
          'abc',
          'xyz'
        ];
[download]