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As far as I know, the replicator reads files from the computer library and based on that pattern it creates the object or food. If it is just materializing objects to the molecule based on that pattern, am I correct in my assumption that if want to replicate say three apples, they would be absolutely identical. Or does the device add some variance? Or are there any limitations which would not make everything identical? And yet, if it introduces some variance, how trustworthy will it be when creating more sensitive items?

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Related: This answer relates the idea that replicators work on a molecular level, whereas transporters work on a quantum level. This allows for imperfections in replicated materials. – NominSim Jan 9 at 3:03
If an answer to this was desired, 'replicator' in the search-field would have immediately produced NominSim's reference. While a question framed more generally would be a nice way to get this answer, 'apples' vs 'latinum' isn't it. – Solemnity Jan 9 at 3:24
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@Solemnity This question isn't an exact duplicate by any means – user11295 Jan 9 at 9:31

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The files from the library may contain either a copy of an apple, copies of multiple apples, or instructions on how to generate random apples. So it's readily possible that replicators could produce random apples.

After all, if you were designing a replicator which makes food for people, you wouldn't want to produce the exact same meal every time as most people would get bored. Built in variety would be a useful feature.

It's probably possible to ask the replicator to produce identical items but it's most likely that the default setting would be to randomise.

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The general dissatisfaction with replicated food might be due to just that: every instance of a meal tastes the same. Hence we see characters preparing meals by hand from replicated (and sometime fresh) ingredients to introduce some variability in taste. – Kyle Jones Jan 9 at 18:49
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Good point but it seems that any designer with an ounce of sense would foresee that problem and build in automated variety. Maybe it's that script writers <> designers. – user11295 Jan 11 at 14:24

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