Hi Paul,
What you need to do is make each Company name a Group and then make these Groups invisible to other Groups.
This way all courses related to an individual Group would not be visible to other Groups.
From memory you can also make Sub Categories invisible too.
Read the Moodle Documents about this.
https://docs.moodle.org/36/en/Main_page
https://docs.moodle.org/36/en/Groups#Why_use_groups.3F
As for removing Menus then I will leave that info to Gareth after you have disclosed to him your Theme & Moodle versions, as that info is theme specific, whereas Groups and Courses are Moodle Core specific and as such are documented.
Cheers
Mary