Fixing permissions

I have run the utility to fix the permissions, but not all the errors are getting fix. How do I change something from rwxr--r-- to drwxr-xr-x. Or how do I change it from rwxr-xr-x to lrwxr-xr-x. I know that I chang change the permissions with change mod, but I don't know what command to get the directory bit to change.

Also, if there is another utility that I should be using to fix the permissions, that would be helpful.