I have following command which tells me File size in GBs which are greater than 0.01GBs recursively in a dir structure.

ls -l -R | awk '{ if ($5/1073741824 >= 0.01) print $9, $5/1073741824 }'

But there are some files whom I dont have enough permissions, after executing this script
gives me error messages.

Now my task is to suppress error messages. I tried with grep -v also.
But it didnt help.

Do you have any solution?

Just redirect stderr to /dev/null, i.e.

my_command_here 2>/dev/null

You could also redirect to a file if you want to check error output later.

Cheers
ZB