If you want to use loops You can try like this: (diff and cmp are much more efficient. )
while read line
do
flag = 0
while read line2
do
if ( "$line" = "$line2" )
then
flag = 1
fi
done < file1
if ( flag -eq 0 )
then
echo $line > file3
fi
done < file2
Note: The program is only to provide a basic insight into what can be done if u dont want to use system calls such as diff n comm..