2001 Audi A6 When changing the brake pads and rotors are there any special tools needed

"Special" tools are not needed. A regular compliment of metric tools, a hammer, wire brush, and cleaning agents should get the job done. As to brake bleeding, I would recommend the purchase of an inexpensive pressure bleeder to perform that task (most German manufacturers recommend a brake fluid flush every two years) Bleeding the brake system is not required if you install new pads and rotors, it is required to bleed the brakes if you have opened the system for some reason such as caliper or master cylinder replacement.