Removing strong pet odors is never easy. The best way to get rid of them is to try products labeled "enzymatic" odor eliminators such as Zero Odor. These products work to break up proteins in urine and fecal material that carry strong odors. Use the product consistently in problem areas and limit your pet's access to these locations to reduce repeat incidents.
For more information, read the articles Inappropriate Elimination in Dogs
and Reducing Dog Urine Odor