I'm assuming the logo is in a raster format (tiff, jpeg, etc)rather than the for more useful and proper vector format (the format in which most professional logos are created). If it does appear to be a vector (generally eps format), you could open in Illustrator and knock out there.
If it's rastere, it's very hard to get a really clean edge when knocking out something, especially if the dpi is rather low. You might try opening the raster in photoshop, upping the resolution dramatically, knocking out what you don't want and then sharpening the edges.
When I've been really stuck with low quality raster logos, I've created paths (selecting the various elements with the magic wand) in Photoshop and the exported those to Illustrator. Then filled in the proper colors. That's the only way I've ever been able to get clean eges that are the strength of vectors.
For some logos, the livetrace and livepaint in Illustrator CS2 can do wonders turning raster into vectors. It takes some experimenting to get good results, though. I find scaling the image up a lot first helps.
You can select the image by using the Direct Select tool. You should get a brownish frame around it. From this you can add and delete points from the frame to make a clipping path, you can move these points around too and adjust them to fit your logo.
The magic wand is a good start to making a selection, but you should perhaps consider making your clipping path in photoshop and then placing the file into the InDesign document.
Once you have the path drawn you can separate the image from the background. Turn off the background and then save it as .psd, place the image in InDesign with the "show options" turned on and select only the layer you wish to be visible.
For this your selection in photoshop has to be perfect.
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