Create the smooth bind
Now, select all the joints from the male_bind_set, shift-select male_geo and in the Animation menu set, go Skin > Bind Skin > Smooth Bind (Options). Now set the following settings and leave everything else as it is:
A couple of notes regarding some of the settings: the Bind Method is the skinning algorithm used to create the bind. The default method is the Classic Linear, also known as Linear Blend Skinning (LBS). I probably use this method 90% of the time but due to the maths behind it, it does cause issues when twisting the joint. (This is referred to as the candy wrapper effect, as the image illustrates, and it is why we have added extra twist joints to distribute the weight). Dual Quaternion performs a different calculation for the bind and is great for reducing the candy wrapper effect but it gives me headaches in areas such as the shoulder and the hips. I tend to find that with Classic Linear, I can get 80-90% of the way there and then additional corrective shapes can finish it off.
Twisting a joint on the X-axis often creates the dreaded candy wrapper effect
Normalize weights set to Interactive will only allow the weight value for each vertex to total 1 (100%). That means if you have 2 joints and you are adding influence to a vertex from either of those joints, every time you add influence from one joint, it will take away influence from the other. If you set Normalize weights to Post, you can go beyond the value of 1 as it presumes that you will fix this later on. I tend to find that I end up with vertices flying around with this setting so Interactive is my preferred setting.
Once you have set those settings, hit Bind Skin and then rotate a few controls around to test out the default bind.
The settings I tend to use for skinning organic characters
Blocking the weights
The next thing I tend to do is to get rid of all the default weights and rebuild everything manually. This is because I like to take full responsibility for the weights, and doing this helps to eradicate any odd floating vertex that can occur from the initial bind. It will obviously take longer to get to the end result but that end result is usually a lot cleaner than simply working on top of the initial bind.
So, start by selecting male_geo and go Skin > Edit Smooth Skin > Paint Skin Weights Tool (Options). This tool here will probably be used for around 80-90% of the skinning process. You'll find all the joints used for the bind in the Influences box and also a selection of options to control the type of brush and the strength and size. I'll be editing the strength and size interactively by holding down the B key (size) and left-mouse-dragging in the viewport or holding down the M key (strength). This is exactly the same as using the Sculpt Geometry Tool or sculpting in Mudbox
Still in the Paint Skin Weights Tool, set the Mode to Paint, the Paint operation to Replace, the Opacity to 1 and the Value to 1. Now select hip_FK_jnt from the Influences list or hold down the RMB over the joint in the viewport and when the marking menu pops up, drop it on Select Influence. With that joint selected, hit the Flood button on the Paint Skin Weights Tool. This joint now has 100% influence over the entire mesh. Try rotating another control and you'll see that it has no effect.
Rebuilding the skinning from scratch
Now, we will let each joint have 100% influence over the vertices that surround it. I like to start from the end of the toes and work inwards but you can also work from the core (hip) outwards. So, select l_bigToeC_jnt for example and then using a flat brush profile, paint over the vertices around that joint. Once you have done so, use the padlock icon to lock the weights of that joint or you can hold down the RMB over the joint and go Lock Influence. Now select l_bigToeB_jnt, paint the vertices around that joint and again, lock the weights. As we do this, we can only ever take influence away from the hip_FK_jnt as we are locking the other influences as we go. Once you have blocked out the left-hand side (we'll mirror this over later) each joint should have 100% influence over a set of vertices.
With everything blocked out, try rotating the joints and see what you get. It will most probably be a very rigid bind but do not fret: this is what we are after. At least we know now that a joint in the arm does not affect a vertex on the chin, or the toe joint does not pull a vertex from the knee.
An example of some of the blocked out regions
Mirror the blocked weights
At this stage, I like to mirror the weighting from the left side to the right side. This model is symmetrical so it should work without any bother, but I've found that the Mirror Weights tool also works pretty well with slightly asymmetrical characters. I say 'pretty well' as you will no doubt have to go in and do some manual cleanup. To mirror the weights, select the mesh and go Skin > Edit Smooth Skin > Mirror Skin Weights (Options). As I've weight painted the left-side of the mesh, I set the Mirror across attribute to YZ and enable Direction. Once you've done this, rotate the same control for both the left and the right side to see if the weighting has cleanly been mirrored.
The settings I use to mirror the weights from the characters left-hand side to the right-hand side