So this sounds like you might be having some retraction based print defects. When the nozzle moves from one part to the other it retracts, travels and then primes again to being printing. This can cause blobs or 'zits' on the outside of your prints and/or possibly strings of filament between them.
There are a couple options in Simplify3D to solve this. The first, and best way, would be to tune your retraction settings for the material you are currently using. ABS can be pretty stringy and might require some more aggressive retraction settings. We have an entry in our
Print Quality Guide that does a great job of covering this. I included the link below.
Alternatively, you could use sequential printing to print one model in its entirety before moving and printing the next. This would eliminate the travels between the parts that are causing the defects. We have a section of our
Multi-Part Printing Article that goes into detail about this tool so I have also included a link to that below but please let me know if you have any questions!