Use Perl.
You need to mirror the hierarchy, and just this will be painful with MS tools. In Perl, you'll find make_tree from the File::Path CPAN package. Also, '-ver' will yield you version extended names, which you need thus to strip from the name of the copies. In fact, if your view doesn't match well with the baseline, you'll get extensions within the path, and my naive example below won't work.
use ClearCase::Argv;
use File::Basename;
use File::Path qw(make_tree);
use File::Copy;
my $bl = shift 'ARGV;
my $tgtbase = '\\\\share\\baselines';
my $ct = new ClearCase::Argv({autochomp=>1});
my @match = $ct->find(qw(. -ver), "lbtype($bl)", '-print')->qx;
my %dir;
$dir{dirname($_)++ for grep s/^(.*?)\@/$1/, @match;
make_tree($_) for keys %dir; #could still be optimized...
for my $v (@match) {
my $tgt = $1 if $v =~ /^(.*?)\@/; #always matches
copy $v, join('\\', $tgtbase, $tgt);
}
Something like that (non tested!).
Marc