As I was getting into 3D printing, I needed a tool to modify objects. Thingiverse has got a respectable library, but not all of the projects are complete...or they don't fit what you need. I covered use of the 3D Print Toolbox plugin in a previous post "Optimizing prints (aka the BB-8 cookie cutter)".
So you'll need a tool. TinkerCAD, AutoDesk, Fusion 360, Maya, SketchUp — they're all possibilities. I chose Blender. It is open source, works the same across platforms (Windows/OSX/Linux), and had more features than I would ever probably use. (This also means that if I needed a tool, I just had to go to youtube and browse.) I could have chosen a simpler software, but then would need to learn a NEW tool when the existing one didn't work.
There are some great tutorials out there. I would suggest searching for the user inventimark - he does covers the basics, as well as going into 3D printing aspects of Blender.
One of the things that we can talk about, without actually teaching you Blender...is the setup. When you start Blender, it'll always use the same basic setup until you change & save it.
First, go to the plugins. There will be a couple I highly recommend — MeasureIt & 3D Print Toolbox. First, we'll go to where the plugins are found. File>User Preferences>Add-ons takes you to the plugins, and you can search for any of the plugins you want to include on starting Blender. (Or you can scroll down, choosing "3D View: MeasureIt" & "Mesh: 3D Print Toolbox".)
At this point if you want to stop, File>Save Startup File will save those preferences.
If you want things in metric, go to the Scene selection (upper right corner), then in the box below choose Scene (currently the middle of 5 options, the graphic is a circle, a cylinder, and a light source. Under Units, choose Metric. Unit scale should be .001. Next, expand the bar to the left of these two boxes (there's a plus sign that you click on to pop out if needed). Scroll down to Display, then change the lines and scale. For my printer bed, I put 200 lines, and the scale as .001. (200mm by 200mm is about the size of my print bed.)
You can save your preferences again, if you went metric.
Your Blender window now has a large grid space, with the thicker lines being centimeters, the thinner lines being millimeters. On the far left edge, you'll notice a MeasureIt tab. The 3D Print Toolbox doesn't appear until you've selected an object (right-click), and then the tab will appear above MeasureIt.
The 3D Print Toolbox has several useful features - Overhang will outline any parts that exceed the setting...I set mine for 45 degrees. When I am in edit mode, and click the "Check All" box, there will be clickable boxes for anything that is found. If you still have the starting square, it will return "Overhang Face:1" and outline the bottom face - it's showing you the bottom doesn't have support, which is correct...it's going to be sitting on the printer bed.
The other useful feature I have needed, was "Thickness". This should be the nozzle of your printer. My Lulzbot Mini has a .5mm nozzle, a lot of other printers use .4mm...this is going to be the thinnest free-standing wall that you can print. I had a BB-8 cookie cutter that I shrunk down, but parts of the cookie cutter wouldn't show up even though they were visible in Blender (and Cura, my printer slicer software). It turned out that the walls were too thin for my "thick" nozzle. Setting the thickness to my nozzle size, it outlines all of the parts that were too thin...I manually adjusted the walls and everything printed just fine.
The final "common" use I have for the 3D Print Toolbox, is great to track revisions. Once you've saved the Blender file, you can click the "Export" button in the 3D Print Toolbox tab...whatever object you have selected will be saved as filename-objectname.stl. This can be useful if you have multiple objects in your blender file, but you want to save/print them as separate objects.