You did not say which version of the program that you are using. Please, always be clear in your questions which program and which version that you are using.
I presume that the program is Audio Cleaning Lab, not Audio Cleaner. I have 2 versions, the latest is 2013. You first have to isolate the part that you want to clean. Use the scissor to cut on each side of the part you want to apply the effect to. Click on this part, which is referred to as an object. Go to the Cleaning part or Mastering part and make sure that you have selected Object and not Project. The effects that you apply will now be to the object selected. Try it out to make sure.
If you later want an effect to the overall Project, go back and verify the result on your object to make sure that this is what you want.
I highly recommend that you read the manual and consult the online (F1) help to fully understand what you are doing.
Here is some text from the online help under Effects Menu:
"Here you will find all effects of the "Cleaning" and "Mastering" tabs, as well as other effects in submenus, which are sorted according to different topics.
If the cleaning or mastering effects are open in Object mode, the effect will be loaded as an object effect, which means it will only affect the selected object and not the entire audio material on the master track."