Not sure I understand your question. If you have a graphic that looks like an isometric cube you just have to align the hitboxes to match the image
Search for voxel (isometric is more like a world with a perspective visualization, while voxel is a volume of pixels within this world, like your cube -- if you know what to search for you will get better results on Google) I like this tool: https://ephtracy.github.io
I recommend you to go through the below link you can simply make isometric with the hexgrid illustrator