Jenn,
The Butterworth filtering available in LabVIEW is designed to accomodate this sort of continuous filtering. If you look at the "Butterworth Filter.vi" there is a control named "init/cont (init:false)" that resets the internal states of the filter to zero when FALSE. So, to filter your large data set pass the data block by block to the Butterworth Filter.vi. The first time the Butterworth Filter.vi is called make the "init/cont (init:false)" control FALSE, and for all subsequent calls keep it TRUE.