You can, but the FX processing for it is quite restricted. You would connect your guitar to the Guitar Input on the HD400. Usually, an acoustic guitar setting uses no guitar amp and a small selection of FX like EQ, compressor, studio pre-amp, and perhaps some chorus, delay and reverb.

The problem on the HD400 is that all of the Comp, EQ, and pre-amp models are grouped together into the FX1 slot, which means you can only use one of those models in any given preset. So you'll have no real problem with applying a chorus (FX2), a delay (FX3) and a reverb. But if you use an EQ (and you can only use one) then you can't use a compressor or the pre-amp, and vice-versa.