Legends
There are depictions in Legends of Force users manipulating microscopic objects.
One example is Darth Plagueis' manipulation of midi-chlorians in order to resurrect a person:
On the same day [Plagueis and Sidious] had allowed Venamis to die. Then, by manipulating [Venamis'] midi-chlorians, which should have been inert and unresponsive, Plagueis had resurrected him.
Darth Plagueis, p. 279
We know that midi-chlorians are microscopic because we are told that
Midi-chlorians are a microscopic lifeform that reside within all
living cells and communicates with the Force.
Qui-Gon Jinn, Star Wars: Episode I The Phantom Menace
Another example, as mentioned in the comments by @BMWurm, is Cilghal's healing of a poisoned Mon Mothma by manipulating individual poison molecules with the Force.
It is not clear which of the two is smaller, though.
Canon
In canon I am unaware of any proven example of manipulating microscopic objects. As far as I can remember, the smallest objects that were manipulated in canon were lightsaber components while constructing a lightsaber:
(H/T @Politank-Z for the video link)
To get a sense of the size of lightsaber components, the schematic of Anakin's second lightsaber from Star Wars: The Visual Dictionary provides a good picture (H/T @WadCheber):
Sometimes small pieces of debris could be manipulated, even in combat -- such as when Darth Maul threw one to open a door in Episode I:
Note that it is possible Darth Plagueis succeeded in manipulating midi-chlorians in canon since Darth Sidious told Anakin that
Darth Plagueis was a Dark Lord of the Sith, so powerful and so wise he could use the Force to influence the midi-chlorians to create life
Darth Sidious (Palpatine), Star Wars: Episode III Revenge of the Sith
However, this isn't a proven example since Sidious may have been lying. Plagueis may not have succeeded in resurrecting anyone because Sidious also told Anakin that
[Plagueis] taught his apprentice everything he knew, then his apprentice killed him in his sleep.
Darth Sidious (Palpatine), Star Wars: Episode III Revenge of the Sith
Plagueis' apprentice was Darth Sidious, but Sidious later told the newly minted Darth Vader that
To cheat death is a power only one has achieved, but if we work together, I know we can discover the secret.
Darth Sidious (Palpatine), Star Wars: Episode III Revenge of the Sith
Sidious therefore lied either in claiming that Plagueis had succeeded or that Sidious had learned the ability from Plagueis. Since Sidious never demonstrated the ability to resurrect others, it's possible he lied about Plagueis being able to cheat death -- especially since Sidious had a motive to lie about it in order to tempt Anakin.