By default in Linux Mint 18.x Cinnamon theme in the desktop system panel is black and opaque. In the settings panel there is no option or setting the transparency panel.

Edit the file default theme’s cinnamon.css with administrator’s rights:

Terminal

Shekin@mylinuxmintpc~$

sudo xed /usr/share/themes/Linux Mint/cinnamon/cinnamon.css

When you open the text editor with the file cinnamon.css, press Ctrl+F in the search box copy/paste the #panel, and then click Find:

Now at the end of this section (panel), add the line (copy/paste):

Terminal

Shekin@mylinuxmintpc~$

background-color: rgba(175,175,175,0.05);

Save the file and close the editor.
To make the changes take effect, you must restart Cinnamon. Press Alt+F2, type r and press Enter.

Now the system panel Cinnamon should be transparent.

Source: Transparent system panel in Linux Mint 18.x Cinnamon