Today I used Netfabb to take a single color object and turned it into multiple objects which I then used Simplify3D to recombine into a multi-color object. In fact, visit our FAQ page to see if you can purchase them. Anyways, to do this, you will first need to install the free/basic version of NetFabb.
The download link is http://www.netfabb.com/downloadcenter.php?basic=1...
Once you have NetFabb Basic installed, find a STL you would like to print; I choose the Leprechaun Hat by MikeT71 http://www.thingiverse.com/thing:727717.
Open NetFabb, go to project > add part > locate your stl.
Your part should already be selected and the cutting window will be on the right. If you're using the Leprechaun Hat, start by right clicking on your part and coloring it green. Next, drag the z-axis cut slider until you are just above the brim of the hat (use the arrows for fine adjustment). Next, click execute cut and then cut. Remember to save lots. Select the top part and do the same for just above the belt.
You'll notice the buckle also got cut; you can't avoid cutting into everything and you'll have to plan out your cuts ahead of time to minimize the number needed. Next, color the middle black. With the middle selected, using the y-axis, align the cut so that it gets as much of the front of the buckle without intersecting the belt. When you execute the cut, ensure you have "only selected parts" selected. Color the new piece gold.
Make another z-axis cut right above the belt buckle, then a y-axis cut right behind the belt buckle. Color the new piece gold. You'll notice that the bottom bit of the clover is still black, this will take about another 3 cuts to fix (depending on how close you want to get). You'll want to make a z-axis cut right below the clover, then a x-axis cut and a y-axis cut. This should give you a few more parts which can be colored green or black appropriately.
Once you're finished with all your cuts, you're ready to start exporting. I would suggest grouping and renaming your objects by color so you don't miss any.
Once everything is cleaned up and ready, right-click each part and click export part > as stl.
I had four green parts, two yellow parts, and three black parts.
Now in Simplify3D, import all the parts, don't worry if they are huge and misaligned.
Then highlight all of them > edit > align selected model origins.
With them still all highlighted > edit > group.
Now double click on a part > scale down and center the object.
Add in three processes, each with a specific tool selected and "select models" for each of the colors green/gold/black. When you "prepare to print", double check you selected the models correctly by changing the "coloring" to be "active toolhead" and then using the time slider to ensure everything will print correctly.
Now just print the object :D. Test it out with different filaments to see what truly works for you.