Dear Bassam, I don't know if you already found how to do sample selection in the meantime, but... anyway: you could use filter_samples_from_otu_table.py (
http://qiime.org/scripts/filter_samples_from_otu_table.html). You can use the script specifying the IDs of the 30 samples you are interested in and obtain a reduced version of the OTU table on which you can calculate beta-diversity and PCO.
Unfortunately, I think there is no way to increase plot resolution in QIIME (I vaguely remember it was specified somewhere in an old post in the forum) and you should export PCO coordinates and plot them in another environment (such as R).
Hope this helps,
Marco