Freelance copy-editors of fiction (such as myself), who work with independent authors, will not generally have the luxury of a structurally-edited manuscript to work on, such as one supplied by a traditional publishing company. This makes our job harder in two ways: 1) It is not possible to fully copy-edit a manuscript without it first having been structurally edited. 2) It makes pricing difficult when having to set a fee for copy-editing that will also include structural editing.
The National Union of Journalists (NUJ) issues an online Freelance Fees Guide. This guide is constantly updated and reflects rates for jobs as submitted by freelance workers. These rates are then used by other freelancers to help set their own fees. The guide covers all kinds of journalistic media (from broadcasting to translation services), to include print media. The NUJ’s Freelance Fees Guide for print media can be found here. In short, the suggested rate, per hour, for substantial editing is £30; copy-editing, £28, and for proofreading, £24. Realistically, actual rates that freelancers charge, for fiction, are likely to be significantly less: for copy-editing, perhaps around £14 per hour; for proofreading, perhaps £9 per hour.
Rather than charge per hour, some freelance editors charge per 1,000 words. I do this. It's easier to calculate, seems a fairer method, and informs the client, from the outset, of how much the job will cost. For new clients, I charge £10.00 per 1,000 words, to include both structural editing and copy-editing. This fee includes all correspondence with the client (mostly via email), and associated documentation. Calculated from timesheets I have kept for previous projects, this equates to an average hourly fee of £15: reasonable, I believe, for my experience, skills, and knowledge, and for the amount of effort I put in. The only additional editing fee I charge is for printing the manuscript for copy-editing and this is calculated at the time, based on the number of pages to print.
Where I contract out typesetting and proofreading, the fee is set by the individual carrying out that job, but I obtain an estimate beforehand.