The motif of secrecy
Throughout the book, the question is always on the table, "Who did it?" But that's not the end of the secrecy and suspicion. The artist left a clue that makes the doctor suspect his secretive patient. The Marques's attempt to obfuscate the evidence for his own purposes raises a lot of questions about what he knows and what he's pretending to not know. The entire tone of the novel is secretive because of this constant motif.
The symbol of the blemish
The blemish itself is symbolic, representing a compromise of the woman's character. Thematically, the idea of a woman going to a doctor in private to address some condemning problem, that idea sounds like a feminist issue, and the blemish removal could be seen as a symbol for abortion. She is going to a doctor for help to protect her honor from some indiscretion of her past behavior.
The image of the portrait
The portrait is a highly meaningful symbol. The face of the painting is obscured, as was the face of the woman from the opening sequence. The doctor removed a blemish from her back, and the artist drew one on. The metaphor is that the painting adequately depicts the Marquesa's character. She is a shape-shifter, and no one can pin down exactly who she's supposed to be, and ultimately, even though her character (the painting) is blemished, her efforts to protect herself seem to have worked somehow.
The allegory of the secretive doctor
The witness to this story is Dr. Malsufrido, well known for his iron-clad ability to keep a secret. When powerful people are in trouble, when they have something to lose, they find him so that he can help them without the whole world finding out. He represents the insight you receive by holding onto a secret tightly, and his revelation of the Marquesa is important. He can see something about her that no one else can because he is trustworthy. He represents good friendship and the willingness to accept people as they are without retribution.
The murder as an allegory
It's easy to forget that the Marquesa probably murdered some poor random guy in cold blood, just to save face. She's likable, so the murder kind of falls in the background. But it's meaningful, because it's what makes her a "femme fatale." The Marquesa is a strangely alluring, powerful woman with seductive magic, and when she murders a victim, it's like a metaphor for when we fall in love with people who are attractive, but will ultimately hurt us. She is like a praying mantis, giving her victims what they want first, before killing them.
