while (<OUTFILE>) {
        s/<br>//gi;
        print FINAL if /(line1)/;
        print FINAL if /(line2)/;
        print FINAL if /(line3)/;

##</code><code>##

This is line1<br>
This is line2<br>
This is line3<BR>

##</code><code>##

$ cat final.txt 
This is line1
This is line2
This is line3