As part of Wednesday’s 41-page federal indictment against Martha Stewart and her former stockbroker, Peter Bacanovic, federal prosecutors spelled out a case that prominently features a blue ballpoint pen.

Or two.

The indictment alleges that Bacanovic altered a worksheet listing the stocks held by Martha Stewart at the Merrill Lynch brokerage firm, including her shares of ImClone. After learning of the Securities and Exchange Commission’s investigation into Stewart’s sale of the ImClone stocks, the indictment reads, Bacanovic added the notation “(at)60” to his earlier notes to give the appearance of a pre-existing agreement to sell the shares if their price dipped to $60 a share. But the blue ink used for the latter notation was “scientifically distinguishable from the ink used elsewhere on the Worksheet,” according to the indictment.

Forensic document experts say the chief method of ink differentiation, known as infrared spectral analysis, has become a mainstay in court cases — especially in medical malpractice suits in which doctors are accused of adding comments to prior reports after the fact.

Dennis J. Ryan, a forensic document examiner based in Merrick, N.Y., explained that the sleuthing can be accomplished by a video camera equipped with a variety of filters and light sources that illuminate the handwriting samples with infrared light.

“Inks that appear blue in the visible range may react differently in the infrared range,” he said. “The video camera is acting like an eye beyond what the eye can see in the infrared range.”

Vickie L. Willard, a forensic document examiner based in Cleveland, said investigators normally look for differences in ink properties, or their chemical signatures, using four types of infrared phenomena. Differences in how the inks reflect infrared light will cause one ink to appear lighter than the other, while differences in how they absorb the light will have the opposite effect, and one ink will appear darker. With another phenomenon known as complete infrared light transmission, one of the inks will disappear entirely. And luminescence can further differentiate among inks, causing one to glow white.

“It’s good evidence when you have it, because you can visibly show the jury, show anybody,” she said.

Okemos, Mich.-based forensic chemist Erich Speckin said a separate process called thin-layer chromatography may have been used to further separate the blue inks, some of which are formulated with up to seven distinct dyes.