Paperwork described any written work that needed to be completed, whether or not they were written on actual paper. It could also refer to specific documents required to fulfill regulations.
In 2004, Loomis used the excuse that he needed the right and complete paperwork from Lawrence Strode to bring him to the blood bank. In reality he gave Strode a sedative and turned him over to the Xindi-Reptilians. (ENT: "Carpenter Street")
Following his cure of the Borg assimilation in 2153, Phlox was doing some paperwork in sickbay. (ENT: "Regeneration")
Captain Benjamin Sisko tried to catch up on paperwork such as criminal activity reports and cargo manifests while fretting about whether or not Romulan Senator Vreenak would discover than an optolythic data rod of a supposed Dominion plan to attack Romulus was a forgery, but found it difficult to concentrate. (DS9: "In the Pale Moonlight")
Kasidy Yates, after having to make numerous reports as a convoy liaison officer and seeing the paperwork that Doctor Julian Bashir had to fill out for Starfleet Medical expressed that such paperwork was the reason she chose not to join Starfleet. (DS9: "The Sound of Her Voice")
Admiral Dougherty told Captain Jean-Luc Picard that he needed his paperwork tomorrow following the capture of Data on the Ba'ku planet. (Star Trek: Insurrection)