Having a heroine adopt male guise has been a staple of the historical tale for quite some time. Shakespeare did it in Twelfth Night, and Georgette Heyer in The Masqueraders and These Old Shades. Kathleen Woodiwiss brought this device to the modern historical romance with Ashes in the Wind. Susan Elizabeth Phillips also had her heroine in male guise for part of her only solo historical, recently reissued under the title Just Imagine. Several romances have adapted or borrowed from the lives of pirates Anne Bonny and Mary Read. As of this writing, there are four newly-released books that have heroines in male disguise in my to-be-read and just-finished-reading piles.
Whether our heroine is out for a lark or running for her life, the heroine disguised as male device is one that can be used in several different settings and eras and for a variety of reasons. In many historical eras, a lone woman would have endured challenges and restrictions that a man, even a young one, would not. Prior to the twentieth century, a heroine who wished to serve in the military had no option but to adopt a male identity, and maritime superstition about women being bad luck aboard a ship (though some captains were allowed to bring their wives) revealed many a cabin boy to be a girl. A heroine who needs to elude captors would be wise to alter her appearance, and altering her perceived gender can throw even the wiliest villains off the track.
The specifics of this will of course vary on geography, era, culture and common dress, but the phrase "If it walks like a duck and talks like a duck, it's probably a duck" applies to disguised heroines. In most historical eras, male and female dress were distinct from each other, and if some form of uniform was involved, the gender of the person in it couldn't be readily assumed.
A woman adopting male guise would have a few things to consider. Her hair would likely have to be cut or at least concealed, and the lack of any form of facial hair would turn even a twenty-something heroine into an assumed adolescent. If she can avoid bathing, a natural patina may have formed, hopefully obscuring a more feminine bone structure as well as smooth cheeks and jaw. Breasts would need to be bound with long strips of cloth such as bandages, unless the heroine has a naturally boyish figure, in which case she might have an extra advantage. Beg, borrow or steal a shirt, breeches and jacket from a likely male compatriot and the transformation is...not yet complete.
Depending on where and when our heroine found herself, she'd need to alter not only her appearance but her speech, vocabulary, movement and social skills. A sailor, for example, would have a different air about him than a gently reared miss of the upper class. If the disguise persisted for an extended period of time, she'd have to find a way to deal with menstruation, and once the hero entered the picture, possibly pregnancy.
Though many women throughout history did choose to live out their lives in male garb, in a romance, at some point, our heroine would resume her feminine appearance. Still, as with when our heroine adopted her disguise, the outer appearance wouldn't always tell the whole story. Whatever she wore, our heroine would have seen life from a different angle, giving her insight into any adventures yet to come.