Note: This is one specific application of the print pausing work of sthone and the thread below, I'm just giving it a separate title so we can find it more easily.
How To- Pausing a Print at a Specific Layer. (Simplify3D)
viewtopic.php?f=3&t=2132
Okay, so to pull off a color swap:
1. Import your file, click on Prepare to Print.
2. Make sure Preview By Layer is selected. Start clicking through the layers using the little arrows or the slider until you determine the correct layer for the color change.
Make note of Layer 5, that's the last solid top layer for the body, (you'll start to see the text). You will want to insert the pause code for the color change 1 layer higher. (Layer 6).
3. Save the Toolpaths to Disk.
Use the SD card that came with the machine, or your own SD card. (You will need a card reader on your computer, or an adapter if you don't have one.)
When you label the file you will have to follow the rules set up below or the machine won't see it:
Maximum of 8 characters, no spaces in the file name.
File extension has to be .g (not .gcode, the default)
4. Find the file on the disk, and double click to open it in a text editor. (I use Notepad.)
5. Click on CNTRL +F to open the Find dialog in Notepad.
6. In the dialog box, type in "Layer X". (X being your layer number.)
Cancel the Find dialog.
Copy the code below, insert a blank line immediately after the Layer line that you found, and paste the code into the file.
G91 ; set relative positioning
G0 Z60 ; raise Z (drop bed)
G90 ; set absolute positioning
M84 S0 ; disable idle timeout
M25 ; Pause SD Print
G92 E0 ; zero extruder
7. Save the file. (File > Save). Eject the disk.
8. Now you can carry the card over to the machine and start the print from the SD card. (In Simplify3D.)
Machine Control Panel > Print from SD Card
9. When the machine pauses for you to make your color change, you will use the Jog Controls in S3D to:
a. Retract the existing filament
b. Load the new filament
c. Extrude enough of the new filament to make sure that your new color is coming out (catch it with tweezers or hold a sheet of paper under it)
d. Clean the tip of the nozzle with the tweezers
10. In S3D, on the Machine Control Panel, click on the Pause Current SD Print button twice to start the print again.
You can insert as many pauses into the code as you like, to create multiple color objects.

If you want to try it with the file shown above, I'll attach it below:
Update: Haven't tested this yet, but apparently, if you are printing over USB, and want to pause the machine manually, drop the bed, change out the filament (quickly, because you won't have disabled the idle timeout), and raise the bed back up; if you send a manual G92 E0 code, it will automatically correct the loading/unloading extrusion before resuming. (per apk
