Feel free to post better ways to accomplish the same things. These are a few things I've learned recently that have made my prints look much better.
Install the newest version - Simplify 3D 2.0.1 is out. If you have Simplify then download the newest version. I don't know how much better it is but I'm sure some things are improved.
Use small layer height and nozzle diameter settings for fine finishes - MAKE SURE YOU KEEP THE "EXTRUSION WIDTH" "AUTO" BOX CHECKED. You can print using settings all the way down to 0.05mm layer height and 0.07 Nozzle Diameter. Using a smaller nozzle diameter setting will give you a much finer print and parts when combined with lower layer heights parts look super smooth. They should rename "Nozzle Diameter" to "extrusion width" since you can print really nice parts with the nozzle diameter setting at 0.07 mm but using a 0.35mm physical nozzle diameter.
Print the first layer thick then subsequent layers as thin as you want. You can print the FIRST layer using a separate "process" with a thicker layer setting and wider Nozzle Diameter setting to take out some of the tedious leveling and Z-offset accuracy required to print very low first layer heights. Think of it as a raft without using the raft setting. THEN, on the subsequent layers make a new process that uses lower layer heights and possibly smaller nozzle diameters to give a fine and detailed finish. The top of the first layer will be level relative to the extruder head so you can print super fine layers without problems.
THE KEY to doing this is using the "start printing at height" and "stop printing at height" settings to tell the slicer when to apply each "process". I don't know why they don't define these by "layer" rather than "height" but you can just multiply the layer height by the number of layers to get the height of any part of the object. Here's an example of using two processes to get a good first layer down followed by very fine print settings without needing to get the bed nearly perfect to start.
Process #1 (first layer)
Nozzle Diameter = 0.35mm
Layer height = 0.25mm
Start printing at (unchecked)
Stop printing at 0.25 mm
Process #2 (first layer)
Nozzle Diameter = 0.15mm
Layer height = 0.10mm
Start printing at 0.25 mm
Stop printing at (unchecked)
When you click on "Prepare" you will see the "Select Processes for Preparation" dialog box. Click "select all" then click "continuous printing layer by layer" to combine the two processes into one gcode file.
Hold Ctrl key and right mouse button to move the object around on the build plate real time (no typing in coordinates)
Hold Ctrl key and left mouse button to scale the object
This isn't a Simplify3D tip but its a good practice to get into...
Mark EVERY spool of filament with the correct extrusion temperature and filament diameter setting for THAT spool. Every spool will have different settings. Sometimes just using a different color may mean you need to use a 10C different extrusion temperature. Measuring the filament isn't really that useful in my opinion. I rarely end up using a filament diameter setting that corresponds to some measurement I get using digital calipers. Print a small part with each spool of material you have. Try different extrusion temperatures and "filament diameter" settings for different layer height and nozzle diameter settings until you get that roll dialed in to near perfect. You can print 10 different calibration parts using 10 different processes using Simplify3D and the "Sequential Printing: Object by Object" setting in which comes up in a dialog box if you have more than one process in place when you click "Prepare". There are many calibration shapes on Thingiverse to use. Once you get it right then write down the best filament diameter and temperature setting for that roll and stick it to the spool. I do this using a label maker to make it easy to read. If you do this you can always leave your "extrusion multiplier setting at 1.00 and you just have to input the correct "filament diameter" setting based on which spool you plan to use.
Defining manual supports - When you define manual supports make sure you have the "Preview" turned off or nothing will happen.
There are more tips but that's enough to get you going for now. I don't know why I didn't think of using smaller "nozzle diameter" settings before now (Head Smack). I hope this helps someone move up the learning curve faster than I have.
The following links are pics of a Christmas gift I printed using the finer settings... The smallest letters are about 2 or 3 mm tall. A very thin extrusion diameter setting allowed me to print small letters with no gaps. BTW, the metal part is cast Bismuth. I made the mold from a 3D printed part. There's a typo that I need to fix but the prints turned out great.
https://www.dropbox.com/s/crwqajgzmoq3h ... rge%29.JPG
https://www.dropbox.com/s/yru9sv3tg68fs ... rge%29.JPG
https://www.dropbox.com/s/phvrw7g56xajh ... rge%29.JPG
https://www.dropbox.com/s/148hnhm1d096a ... rge%29.JPG