If I now read this file into an array and then try to grep the array index, it just doesn't work.

See also How do I post a question effectively?.

Update: please mark your updates (like I did this one) and use <code> .. </code> tags to mark your code. it makes it a lot easier to read (and type). See also writeup formatting tips.

Anyway, I'm assuming you've omitted a few pieces in that code snippet that are actually there in the real code (like the part where you write to "clean_text").

Note that

my(@lines) = <MYINPUTFILE>; # read file into list
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I also note that it's very likely the lines have other whitespace in them. It's probably easier to match using a regular expression:

# match the string "foo" on "word boundaries"
my @line_numers = grep { $lines[$_] =~ /\bfoo\b/ } 0 .. $#lines;
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# match lines containing the single word "foo",
# ignoring whitespace
my @line_numers = grep { $lines[$_] =~ /^\s*foo\s*$/ } 0 .. $#lines;
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"Is there any hope for me?" Probably.

What do you mean by "grep the array index"? Do you mean "search the array for the index of an array element containing a specific entry?"

I'm guessing you're doing something like this to read the array:

open(my $fh, "<", $stripped_file) or die "Could not open $stripped_fil
+e because $!\n";

my @text = <$fh>;
close($fh);
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It would be helpful to show us some code and a sample of the stripped file.

And if your data is in an HTML table, you can get your array in a single line of AnyData code. AnyData uses both LWP and HTML::TableExtract under the hood:

use AnyData;
my $arrayRef = adConvert(
    'HTMLtable',                  # input is an HTML table
    'http://host/path/foo.html',  # input comes from a remote file
    'ARRAY',                      # output is an Array reference
    '',                           # output not sent to file
    {count=>1}                    # HTML::TableExtract flags
);
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$append = 0;
if ($append)
{
open(MYOUTFILE, ">clean_text"); #open for write, overwrite }
else
{
open(MYOUTFILE, ">>clean_text"); #open for write, append
}
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looks like you are overwriting if $append is true and appending if it is false. Perhaps a little misleading?

The use of the three argument form of open is to be encouraged as is the use of lexically scoped filehandles. You should also test that the open succeeded. Most importantly, putting the lines use strict; and use warnings; at the top of your scripts will save you a lot of wasted time in the long run as it will help you spot typos like

$append = 1;
...
if ( $apped )
{
    # Append to my file
}
else
{
    # Trample all over my irreplaceable data
}
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Using strictures, three argument open and lexical handles your piece of code might look like

my $append = 0;
my $cleanedFile = q{clean_text};
if ( $append )
{
    open my $cleanedFH, q{>>}, $cleanedFile
       or die qq{open: $cleanedFile for append: $!\n};
}
else
{
    open my $cleanedFH, q{>}, $cleanedFile
       or die qq{open: $cleanedFile for overwrite: $!\n};
}
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I hope these thoughts are of use.

Cheers,

JohnGG

use AnyData;
my $arrayRef = adConvert(
    'Text',                       # input is plain text
    'http://host/path/foo.html',  # input comes from a remote file
    'ARRAY',                      # output is an Array reference
    '',                           # output not sent to file
    {eol=>"\n"}                   # define the eol for reading input
);
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update : but, um, duh, that won't let you strip the HTML so, nevermind, but if your data is in an HTML table, the solution below would work.