How do you perform a clean install of macOS High Sierra with APFS?
This can be done by downloading the High Sierra installer from the App store and use it to create an installation USB media.


Locate and install macOS High Sierra in the Mac App Store.
Plug an empty USB flash drive into your Mac with at least 12 GB of space.
Run the following command in the terminal:

sudo /Applications/Install\ macOS\ High\ Sierra.app/Contents/Resources/createinstallmedia --volume /Volumes/MyVolume


Where MyVolume is the name of your USB flash drive.
Leave the USB drive plugged in and reboot your Mac while holding the option key (ALT) down.
Choose the installer from the boot menu.
From the installation environment, choose to install High Sierra on your internal disc. The installation should default to APFS.


A more detailed explanation can be found on the Apple support page: How to create a bootable installer for macOS