3dmerge has a new option:
-1filter_blur 12.0
to do Gaussian blurring with FHWM of 12 mm (for example). This filter (unlike -1blur_fwhm) will obey the mask given with -1fmask.
You need the latest AFNI update to get this feature. If your '3dmerge -help' doesn't say anything about '-1filter_blur', then you are behind the times.