How to pick peaks in a 3D spectrum

Typically, picking a 3D is done after or based on a 2D spectrum that is a projection of the 3D. For example, for 3D 15N edited NOESY/TOCSY or triple resonance assignment spectra, it is usually most efficient to pick in a directed fashion using the 2D 15N HSQC as a guide. Analysis offers a number of ways of doing this.

Semi-automated, user guided - LinkPeakLists popup
Peak pick and initialise the assignment of the HSQC followed by using the LinkPeakLists popup (see Peak Picking and Manipulation and Efficient Resonance Assignment in the analysis tutorial).

Automated, directed - pickAssignSpecFrom2dRoot macro
Peak pick and initialise the assignment of the HSQC followed by using the pickAssignSpecFrom2dRoot macro (look in the Macros popup accessed via the Macros main menu item). You can use the functions that are the guts of the LinkPeakLists popup without the GUI. You might want to do this if you are aiming for highly automated structure determination with minimal user intervention, but you need to tune the "peak find" parameters carefully before embarking on this course.

If you want to just pick all the peaks in a spectrum in an undirected way (do you really?) there are a number of ways of doing this.  The most intelligent way would be to use the Region Peak Find popup (under Crosspeaks on the main menu) so that you can at least exclude water stripes, regions with many artefact peaks etc. Take care to tune your "peak find" parameters.