Remove CiviCRM logo from Invoice pdf?
The invoice is generated based on the template "Contributions - Invoice". It contains a line to the logo ({$resourceBase}/i/civi99.png" height = "34px" width = "99px") that you would need to replace.

You can find teh message templates by Navigating to >>Administer >>CiviMail >>Message Templates in the tab "System Workflow Messages"