this is NOT a good idea...
Quoting the above:
• Preserve the exterior surface and the end grain: Saw off any uneven board ends, then plane each side of the boards before running them through the jointer. These steps will put a nice, even finish on the lumber.
If you mean "hand plane" then that's a different story, but even a small nail will ruin a beautiful edge on a hand plane. If you mean use a thickness planer, then it is NOT a good idea what so ever. It's best to cut away any potential pieces with nails. You will also lose any patina, coloration and texture which are often the reasons for using reclaimed lumber in the first place.
If running the boards through the thickness planer to clean them up or make them a uniform thickness is the goal, then that's a different issue.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)