It means "How do you like it cooked?". For example, being beef is you choice of meat, you can then further choose to have it grilled, fried, boiled, steamed, etc.. Or, even further, you can name the dishes that you want, as for each of these cooking methods, there are hundreds of dishes combination, like "steam beef with bean", "boiled beef with pepper", etc.

it means how to cook the meat,frying ,roasting,bating or boiling,haha ,many kinds

这里有鱼，你喜欢怎么吃=There are some fishes, which cook style would you like?

i think it means how to cook it you like best. for example.you could roast meat or boil meat. it depends on you.

“怎么吃？”常用的有两个含义： 一、如何制作食物。比如，今天买的鸡怎么吃？烤着吃。 二、做好的食物要用什么样的方法吃。比如：这种面包要怎么吃？要抹上黄油再吃。