Working with Nova's .3di files is a post-apocalyptic nightmare where resources are scattered and only a few old dudes in remote cabins know anything about it.
Each game has different tools - mostly unofficial - that serve different purposes.
DF1
DF2- FwO Raven's 3di Viewer - view items, export meshes to .obj, export textures
- NovalogicTools - unofficial mod tools for DF2 which includes a .3di viewer. This one requires some legwork since you'll need to compile the source code as no binaries have been released.
- Nova3diLab - my own tool for converting .mqo files to .3di files. See releases for downloads.
- A 3di plugin for Ultimate Unwrap 3d for viewing. Will share link once approved by staff.
DFLW
BHD/TS
Joint Ops
Multiple Games
As you can see, the majority of tools are for viewing items. Nova's official mod tools for BHD+ are your best bet for importing custom models. My Nova3diLab for DF2 is the only pre-BHD tool I know of for importing models, and it's pretty experimental.