Hi @DarkStar ,
So what it looks like here is that you are trying to soften or ease the transition between pieces of hard surface geometry after you fuse them together. Hard surface work typically has some additional concerns, and requires you to more carefully manage your topology. While you may be able to achieve satisfactory results using “quick and dirty” methods at high resolution, taking the time to create high quality topology for your model will ultimately give you the best results and the finest control. It’s likely that either approach will have you frequently shifting your topology at different steps in the process.
Please keep the following general principles in mind:
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When working at high resolution , the detail and crisp edges are maintained by the dense geometry there. As you remove points from the mesh, you will also lose form and detail. So in the case of hard surface meshes, it’s important to reduce the geometry into a form that results in edges being deliberately drawn along the natural edges of the mesh so that they can be marked for creasing. Otherwise the form of the mesh will smooth itself away when subdividing up from low poly to re-smooth it.
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The form of any mesh can be expected to smooth itself when it is subdivided as long as SMT is active, unless an edge is creased or there is dense geometry there to maintain the detail. The lower poly the mesh is when subdivided, the stronger the softening of the form will be. This can be used to create soft transitions by simply defining the areas you wish to stay sharp and subdividing the mesh. Transitions and edges will naturally smooth themselves unless specifically protected or reinforced with additional topology. Two edges placed closely together are the same as a crease, and can be moved farther apart to soften the edge.
It’s an old ZBrush trick to subdivide a mesh partially with creased edges, then eliminate the creasing and continue to subdivide. This produces softened edges that are still well defined but not impossibly sharp.
- You can mask an area of the mesh to protect it, and smooth the unmasked portion with various sliders in the Tool> Deformation palette. Your results here will be dependent on the quality of your topology and your ability to isolate the geometry you want to target for smoothing. Polygroups are going to be extremely useful here, as are the various shortcuts for quickly hiding sections of geometry:
http://docs.pixologic.com/user-guide/3d-modeling/modeling-basics/polygroups/
http://docs.pixologic.com/user-guide/3d-modeling/modeling-basics/mesh-visibility/
http://docs.pixologic.com/user-guide/3d-modeling/modeling-basics/masking/
You would have the finest control and the cleanest results by converting your mesh into a low poly form with very clean topology and polygrouping. This can be done with ZRemesher and well defined polygroups. However it is a broad subject in itself, requiring you to be comfortable with Zmodeler and low poly modeling as well as the ins and outs of using ZRemesher to reduce and simplify geometry.
A quick and dirty approach I might recommend here when working at higher poly is to use Bevel Pro. Bevel Pro can create bevel geometry to serve as transitions for complicated mesh intersections. These can be applied to the mesh to change it directly, or imported back into the program as a subtool to be used in a non-destructive Live Boolean process. All you have to do is group the the sections you want to create bevels between into separate polygroups.
You can then use ZRemesher to simplify and clean the topology, which can be further subdivided and smoothed.
Please see the following image, and forgive me for creating such a simple usage scenario. The problem with this simple case could be easier solved a half dozen other, faster ways. Your problem is that you are fusing separate pieces of high resolution geometry with a very complicated intersection, and don’t have access to clean, simple edge loops to edit the polygons directly with modeling operations. I am merely using this case to illustrate the process.
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In this image you see we have two primitives that have been fused together with Live Boolean. This leaves the topology mostly unchanged, but creates extreme triangular geometry at the intersection. This type of geometry will cause problems when attempting to sculpt, smooth, or subdivide it. Unless you are simply going to decimate and export, you may want to clean this if you are going to work with it further.
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I use Bevel Pro to create the transitions, apply changes and hit “ok”.
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This is the resulting mesh. You see the same problem geometry at the intersection. If you’re going to do anything else to this mesh you will probably want to clean it up, and doing so will provide you with more opportunties to smooth and shape the geometry.
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I use Zremesher with the Keep Groups option to simply the geometry and return it to clean quads. Main points here:
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ZRemesh at high target polycount to start, then reduce with “half” option until you start to lose the form.
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Local flaws in the topology are usually caused by tiny polygons near a border that may have a stray polygroup. May not be able to be seen unless you smooth the mesh. Use Dynamic subdivision to help you preview what the mesh will look like when smoothed. Being comfortable with Zmodeler will let you touch up problem areas on the fly.
Once ZRemeshed, now I have nice clean quad topology and clean edge loops that I can manipulate or delete to shape the transition further. Subdivide to smooth.
Good luck! 
