The instructions of the engineering journal I submitted to (IEEE transactions on wireless communications) says this regarding the final submission of figures and tables
Please upload the Originals (masters) of the tables and figures (in separate files, one
figure per file). All graphics material submitted for publication must
be original drawn figures in .eps format, with each figure submitted
as a separate file. Figures exported from other formats (e.g., PDF,
PowerPoint) will not reproduce well in print. Appropriate fonts
include: Symbol, Helvetica, Arial, Times New Roman.
What do they mean by "originals (masters) of the tables"? Does it mean that I should submit each table also as a separate file? If so, in which format?
In my opinion, the guideline regarding tables is outdated, and one can safely ignore it. If you submit your manuscript in LaTeX, put your tables in the main text. This is a current mainstream in (STEM-related) journals, and it is good to delicately push IEEE towards it. In case if they insist on doing this the other way (which I seriously doubt), you can address the questions to their production team.
The guidelines aren't very precise, but this is what it means:
Submit your tables in separate files, one table per file, but only if the tables are floats (which virtually all tables should be anyway). The placement of these tables will depend on the journal's typesetting of the text in your document. They are very unlikely to end up where you put them in your text anyway, so it makes sense for the typesetters to insist they don't appear in the text in the first place. It's typically enough to put all tables at the end of the document, with one table per page. You can do this with the endfloat package in LaTeX. If the journal really insists that tables should be submitted in separate files, you can use the standalone package. I sincerely doubt that tables need to be submitted as .eps files. Tables are text, not graphics, and your guidelines only say that "graphics material" need to be submitted as .eps. Submitting them as .pdf should suffice. The typesetters will create your tables from scratch anyway.
Figures are another matter. The typesetters will not alter them at all, they will simply insert them into the document in the place deemed most appropriate. You need to create your figures as .eps files and submit them as separate files. If the software you made the figures in doesn't include .eps as a native format, use tools such as ps2eps (if your software includes .ps as a format) or pdftops (if your software includes .pdf as a format) to convert your figures to .eps.