For the simple case:

#! perl -slw
use strict;

my $str = q[
first line
#ifdef ABC
second line conditional on ABC defined
#else
second line conditional on ABC not defined
#endif
#ifdef PQR
second line conditional on PQR defined
#else
second line conditional on PQR not defined
#endif
third line
];

my $macro = 'ABC';

$str =~ s[
\#ifdef\s(\S+)\s+
([^\n]+)\n
\#else\s+
([^\n]+)\n
\#endif
]{
    $1 eq $macro ? $2 : $3
}xeg or die 'No match';

print $str;

__END__
C:\test>junk7

first line
second line conditional on ABC defined
second line conditional on PQR not defined
third line
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