It means to set a certain permission on the file or directory. The most common chmod commands are 644, 755 and 777.
You can chmod in Cpanel in File Manager by selecting the file and clicking on "Change Permissions".
To chmod a certain file or a category using an FTP client, find something like "Change File Attributes", "Properties", or "Chmod" and enter the chmod command script instructions tell you.
Permissions:
u - User who owns the file.
g - Group that owns the file.
o - Other.
a - All.
r - Read the file.
w - Write or edit the file.
x - Execute or run the file as a program.
Numeric Permissions:
CHMOD can also to attributed by using Numeric Permissions which are summed together:
400 read by owner
040 read by group
004 read by anybody (other)
200 write by owner
020 write by group
002 write by anybody
100 execute by owner
010 execute by group
001 execute by anybody
Example: Read by Owner+write by owner+execute by owner+read by group+execute by group+read by anybody (world)+execute by anybody (world) = 400+200+100+40+10+4+1=755