If I understand what you are saying, the way you trigger an acquisition should have minimal effect on the techniques you can use to denoise the data. You can do a running average, a median filter or even use some of the more advanced denoising techinques discussed in books such as Tukey's "Exploratory Data Analysis" (an excellent book, by the way).
In terms of code for doing the processing, building a running average subVI used to be one of the standard examples used in the LV training classes so there are dozens of implementations around--or you can build your own in about 5 minutes. The median filter is part of the "pro" version of LV. Beyond that I can send you stuff based on Tukey's work if you like.
Mike
mporter@arielcorp.com
