Nautilus is the file manager.

Nautilus was started by a former Mac developer in the 90's. Becoming proficient with the file manager is one of the key ways that you can become more efficient.

Click on the above image for a larger version

Starting from the top left of the interface....

1. Back and Forward buttons are super handy if you want to go somewhere you just were. Keeping this window open means you can go to the source folder and copy to the destination then go back to the source. Like on the internet it keeps a history of places you have gone to.
2. The top half of the side pane contains...
3. "alfred" or "your name here" is your home folder.  This folder contains your Desktop folder and all your documents
4. Desktop (desktop icon) - your desktop folder
5. File System (drive icon)  - You will rarely need to access this, this is ubuntu's root directory. 
6. Connected drives, including
   
   1. Windows Shares
   2. USB Sticks/flash drives
   3. FTP/SFTP connections
   4. Remote Office Connections
7. Bookmarks  (bottom half of the side pane) - this is one of the most handy places. Bookmarks make it easy to make shortcuts to places you visit often. Even if it is just for a current project, you can make a shortcut and then remove it later.
8. The side pane can have other info windows as well - more details below..
9. Don't forget the empty space area where your files and folders are -  this empty space is useful because you can right click  and create folders or documents, access the items properties, etc.
10. The big foot is just a notification system to show you the manager is busy
11. List and Icon view. They each have their advantages.
    
    1. Icons - gives you more blank area to click and do actions; allows you to see thumbnails of images.
    2. List view lets you see more info and more files all at once.
12. Search Need to find a file?  This is where you click. There are lots of options but the first window is basic enter the name or words of the title of the file. More on this in the Search Tool below
13. Reload can help if you just made a file/folder and it is not showing up.

Using Nautilus Bookmarks -

1. this is where you work flow is made efficient. If there are places you need to get to then bookmark them. Just click Bookmarks > Add.  Notice the menu tells you where the keyboard shortcut is as well, in this case Ctrl+D.  Almost all menu items have shortcuts that save time. So if you are in a folder and want to add the folder to your bookmarks just click CTRL-D.
2. The next question is how to organize them. As you see in the above menu there's the Edit Bookmarks option (CRTL+B). This is where you can put rearrange your bookmarks, or rename them.   You can also rename and rearrange your bookmarks by right clicking on them in the left side pane, but be careful not to inadvertantly drop one folder into another when using this method. 

There are lots of options here. The default are good but if you want to always see List view or change the color of the background here is where you go.  To access the preferences menu choose Edit > Preferences

1. Look over the other tabs as well.
2. Also there is Edit Back and Emblems to make it look a bit nicer. More on emblems in the Info window area below.
3. Info Window Area - I do not use these tools / features a lot but I think they could be of use.
   
   1. Click on the Places Menu and you will see a list.
      
       
4. Key Short cuts
   
   1. When you enter a folder you can type the letters in the file you are looking for. For example if I go into my documents folder and I know I want NPP I just type it and the folder will be highlighted, then type Development and enter and it is highlighted etc. This is the quickest way to get to your files w/o the mouse.
5. Right Clicking on Files
   
6. Properties of a File