In my experience copper will harm the biofilter, although it will bounce back given time. Copper is stressful to many species of fish also.
In particular angels and some species of clowns, will not tolerate therapeutically effective levels of copper and will be severely harmed or killed. Having said that, copper can be extremely effective and many of us have snatched prize specimens back from death's doorstep with it.
Out fitting your quarantine tank with a diatom filter and/or an oversized UV sterilizer is an extremely effective method for eliminating parasites! Without the use of toxic meds, a small fully functioning reef tank (with no fish) can be used. This further minimizes stress to the fish and gives it a much better chance of acclimating to a captive environment. Usually a three to four week stint in this type of setup is adequate to eliminate most parasites. In my opinion these two pieces of equpment are much underutilized by the hobby (probably due to cost).
On the rare occasion where this does not work one can then resort to using the usual chemical agents, sans the UV of course! A diatom filter is OK to use in conjuction with medications.
Hope this helps!
Cheers!
T
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