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I cleaned my dirty sensor of nikon d3400 few days back and the dirt spots are gone now. But a random thought came to me which is troubling me now. I wanted to know if cleaning the sensor could alter the auto focussing abilities of the camera for example somehow some layer is build on the sensor after cleaning which can cause the camera to set different settings for iso, aperture and shutter. I forgot to take pictures of a sample object before cleaning so that I could compare by taking the picture of the same object in the same light conditions after cleaning.

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On most DSLRs, focusing is done through a dedicated phase detect sensor which is separate from image sensor. As a result, autofocus is not impacted by anything you to do the imaging sensor.

This image (source) shows the various parts of a DSLR: DSLR cross-section

#2 and #3 are the parts of the mirror mechanism which fold away when creating the image. The light that enters the sensor is partially reflected upwards to the viewfinder (#9), and the other part is reflected down to the phase-detect sensor (#7). As you can see, this is completely separate from the image sensor (#4).

As an aside - fluids for sensor cleaning are specially designed to not leave residue on a sensor. If you used a sensor cleaning fluid rather than standard alcohol, this should not be an issue.

For mirrorless cameras, autofocus is performed by the same sensor as the imaging. Contrast-detect autofocus (CDAF) works by maximising the contrast within the selection rectangle (which is why it works best on hard lines). CDAF is not, in my experience, greatly worsened by a small decrease in contrast in the image.

Mirrorless cameras with onboard phase-detect autofocus (PDAF) exist, but I cannot comment on that.

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    I would say that cleaning the sensor can cause issues with PDAF... it is quite possible to "relocate" dust/debris and for it to fall on the PDAF module's lenses. Almost no-one mentions cleaning those while you're in there; but if they get dirty enough, it can really mess up the AF. – Steven Kersting Jun 21 at 14:41
  • @StevenKersting Is there not a double-sided sticky tape that works as a dust trap? This is how it worked on Oly DSLRs and now on their mirrorless cameras. – wilkgr Jun 21 at 22:40
  • @Steven thanks for the info – Neetu Jun 22 at 13:20
  • @wilkgr, most cameras that have automatic sensor cleaning also have a "dust trap" to collect whatever is shaken off. But that doesn't prevent the PDAF lenses from ever getting dirty/obstructed. – Steven Kersting Jun 22 at 17:11
  • @StevenKersting thank you for the explanation! – wilkgr Jun 22 at 23:21
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No. Cleanliness is next to godliness, and godliness is next to good autofocus.

Having a clean sensor will not be a detriment to autofocus algorithms.

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