THESE ARE confusing times for aliens. Many millions of undocumented workers in this country were expected to apply for amnesty under the terms of the immigration law passed last year. So far, the numbers have been disappointing, perhaps because some aliens do not understand the details of the program and others fear the consequences of coming forward. All need to be reassured and encouraged.

Congress understood that some would-be applicants would be reluctant to present themselves to immigration authorities for fear of being rejected and deported. To overcome this apprehension, two important provisions were added to the law. The first authorizes a network of non-government agencies -- churches, social welfare groups, ethnic organizations -- to accept applications and to do the initial paper work. The second provision forbids the use for any other purpose of information learned through an amnesty application. This protects applicants against criminal charges for using false papers to get a job, for example, and it protects them from deportation based only on this kind of information.

Most recently, aliens hoping to qualify for amnesty have faced new problems. Some have been fired from jobs they have held for a long time because employers believe they will be penalized for hiring illegals. The catch here is that an applicant must show he is self-supporting to qualify for amnesty. Employers are being reminded by the Immigration and Naturalization Service that they need not fire workers hired before the law was passed last November. And fortunately, in tough cases where an applicant can show a steady work history that has been interrupted only because of an employer's misunderstanding of the law, a spokesman for the INS says, the government "will give applicants the benefit of the doubt."

AIDS testing is another worry. This country's immigration laws have traditionally barred admission of those who have contagious diseases, and newly announced regulations make clear that this restriction will be applied to those who carry the AIDS virus. Applicants for amnesty will be tested, and under the law, those who have the AIDS virus will not qualify for the benefit. But the attorney general has given assurances that such people will not be deported because information about their medical condition learned during the amnesty process cannot be used to penalize them.

Much public and private energy has been devoted, in recent months, to helping those aliens who will qualify for amnesty. It is sadly true, however, that there will always be some who prey on the desperation of those who come here illegally and who seek to exploit their vulnerability. This week, in Brooklyn, 21 private security guards and six others who helped them, were arrested and arraigned on charges of extortion. They had all, it is alleged, engaged in a scheme to coerce individuals awaiting deportation who had been placed in their custody. It is charged that large money payments and sexual favors were demanded in exchange for arranging an alien's escape and that food was withheld from those who refused to cooperate. Abuse of people who are so desperate and so vulnerable by those in authority is despicable; if the charges are proved, the punishment should be severe.