How to visually search for specific parts in a 3D model? For a missed/loose piece that needs to be reattached, I plan to check all the steps where the piece was used. If I can also get an overview of the possible piece locations from the existing 3D models, that should speed things up as well. However, I don't see any option to filter/show by piece in Mecabricks or LDD. Is there any other way?
Okay Bro, here we go.  I still use LEGO Digital Designer.  Open it, and you'll be using a combination of a few tools to filter out the exact piece locations in your model's 3 dimensional space.

Below we'll use pictures of Bowser as an example for a few selections.


The "Selection" tool sub tools:

(1) Single Selection: Pick one piece you want to move.

(2) Multiple Selection: Pick multiple pieces you want to move. Shortcut Key:  Hold down control button to to select multiple pieces. 

(3) Connected Selection: Move the pieces that interlock in a continuous cluster. (VERY USEFUL FOR ME!)

(4) Color: Pick a specific color.

(5) Shape: Pick a specific shape REGARDLESS of color.

(6) Color and Shape: Pick a specific shape and color.

A combination of two other tools that will bring it all together is the "Invert" Selection Tool and the "Hide" Section tool.  

Connected + Hide Example:

In this example of "Connected" Selection, look at Bowser's toes.  They're not highlighted, which means they are not connected, but after we hit the "Hide" button we see a green piece of Bowser's chest just a floatin' too.

Connected.


Hidden.

Multiple Shape + Invert + Hide + Shape and Color Example:

I buy my models on Bricklink.com but have to upload them through Stud.io, but Stud.io doesn't recognize which 1x1 tiles LEGO Digital Designer is using.  So, I have to filter them out regardless of color, and figure out how many of each color I need to manually add them to my purchase later.

Selection of 1x1 tile regardless of color.


Invert Selection.


Hide non 1x1 tiles.


Specific Color and Shape for PINK.  Lower left corner tells me exact amount I need in this color.


Specific Color and Shape for GREEN.  Lower left corner tells me exact amount I need in this color.


Specific Color and Shape for TAN.  Lower left corner tells me exact amount I need in this color.

With these combinations you should be able quickly see and fix your shit!  Good luck and Later!