Is removing items from meals allowed?

I should be going to Tokyo soon, but reading the etiquette guide worried me a tad,

See, I dont like eggs, but they seem to come hard boiled in some soups and noodle dishes,

Anyway, Is it bad manners to take the egg out of the dish and leave it to one side, or should I leave it in the bowl and have to eat around it?

Serin,

No, I don't think it is bad manners at all.

I don't think it's a problem. I work as a waiter at an Italian restaurant here in Tokyo and it's not rare for customers to ask for things to be taken out of their meal. Maybe a very traditional Japanese might be a little different, but not usually a problem here. The Japanese saying "Okyaku-sama ga kami-sama" means "Customer is God" so customers can pretty much do what they like and be treated with respct. Don't abuse that, but know that you're unlikely to get abused for a simple request to hold the egg. If your request is refused, it'll probably be because the dish is pre-prepared or something (unlikely in the case of a egg being added).

I think it's not polite to REMOVE an item from your already prepared dish.

However, there is no problem requesting the chef or waiter in advance NOT TO PUT an item in your dish in the first place.

Or if you fail to ask in advance, you can request the waiter to remove an item from your plate BEFORE you start eating it. That way, the item may be used for something else.

Keep in mind that it is basically polite to finish everything on your plate. Moreover, you will be wasting the crop of the earth if you don't eat something that is already served. The same can be said when eating at someone's homes.

My family is allergic to eggs, and we make sure as soon as possible that eggs aren't included in the meal.