There's a number of 3D applications that I use.
VRoid Studio is an anime based 3D character model "tweaker". Most of the hard work is already done for you, all you do is tweak the settings. The most powerful part of this program you can draw the hair and style it pretty easily, although, it can get complicated, but looks fantastic! This is a free program.
I've also used
Unreal Engine, while this is primarily a video game creation tool, you can create 3D worlds within it. It has a pretty unique visual scripting language, you right click for the commands and drag and drop the lines to the pins for what you want the commands to do. There's tons of YouTube resources available. It's also free. You can use Unreal Engine to create entire movies!
Blender 3d is another program that's free, and is extremely powerful. You can use Blender to create clothing and anything else in a 3D environment. Lots of tutorials are available.
These are three that I've used, not very much, if I had more time to invest in playing around, I would totally love to create my own world and characters!
One other shout out to
Booth. This is a 3D model asset site that you can purchase and sell your 3D creations for cheap (like 300 yen (about $3.00) is a typical price. You can also find lots of assets in the Unreal Marketplace, including plants, and natural materials to build a 3D world with.
There's a ton of other programs available, some include Maya, WorldBuilder, Gaia, 3DStudio Max, and others. Each of these programs are made specifically for certain types of 3D building. For example, Maya is built specifically for characters and humanoids. 3D Studio Max was created primarily for architecture and blueprinting. And Worldbuilder and Gaia are used to create randomized landscapes with ease.
One thing I've thought about is writing a fan fiction, and then transforming that into a 3D world, making my own anime out of it.