Is there any way to select vertices and then align them along the x,y, or z axis? So as to take willy-nilly sections of the model and smooth them out precisely. I am trying to ease my model into transparency along the z axis, and it would be easier if I could select a point, then line up the row of vertices to it, rather than pushing each point into place manually. Thank you, I hope this question is clear!
There are several ways to go about aligning vertices, best would be a combination of these for either organic or hard surface modeling. For your use case, the first should suffice.
Select the relevant vertices and scale while constraining to an axis, change the Transform Orientation so it aligns as you want it.
Enable Snapping, select the Snap Element and adjust accordingly.
Smooth the mesh pulling the vertices closer to each other.
Here are a couple of ways to do this, starting with the common quick way:
Quickly align to Global X, Y, or Z
Select the verts you want to align. If they are all on the same edge you can select the edge loop from the Select menu.
Scale on the axis you want to align them all to, and type "0".
Type in a location value for that axis. I find aligning to 0 first, and then positioning, to be sufficient for most cases.
However, there are times when you'll want to use the 3D cursor instead of aligning first and then positioning.
There are also cases where you may want to use a custom axis (transform orientation). The following method describes how to do that.
Align to a custom Transform Orientation
In Vertex Select Mode, draw an edge
You can use Ctrl+LeftClick to create and then extrude vertices.
Then, with the entire edge selected, snap the Cursor to Selection using ShiftS
With the edge still selected, click the "+" button in the Properties Shelf under the Transform Orientations panel.
Click the Transform Orientation button which is by default set to "Global" and choose "Edge".
Scale along it
You can now hide (H) or delete (X) your guide edge.
In the image above we see starting shape in gold circle.
Finished shaped in blue modified circle highlighted vertices.
Pivot around 3D cursor as indicated by lower golden arrow.
Vertex is selected. Shift-S [Snap cursor] to selected.
This is indicated by the upper golden arrow. Small Cursor require effort to see.
Select more vertices.
Keystrokes SZ0. Scale Z Zero.
Scaled vertices have same Z value as Cursor.