Hi Michael,
I guess there are more than one way to do it.
One way is editing the VIH (initial head file) file directly. You may
need to do some testing and see how rows and columns are counted in
VIH as it is not documented in the user manual. Then you may need to
write a script (e.g. macro) to convert your initial head data into
appropriate format.
Another simplier way is using Groundwater Vistas. Its import and
export functionality is much better. You can simply import you initial
head data into Groundwater Vistas and then export it as a head file.
Then you can use the head file as initial heads in VIsual MODFLOW
directly.
Hope this helps.
Kind regards
Chris Li
Groundwater Modeller
Department for Water, South Australia