Hackers can gain access to your system manually or by infecting your computer with malicious code. The latter method is currently in vogue. Malicious code can be extremely hard to detect. If a hacker is serious about attacking your system they can execute what is called a kernel based attack. The kernel is the brain of your computer, it is where the operating system or OS resides. Most software you can buy or download is not able to access the kernel so when a hacker performs a kernel based attack, they are incredibly hard to counter. By embedding themselves inside the OS, they are able to bypass encryption and firewalls and access raw data as it passes through the operating system.
Trojans, malware, viruses and worms are all ways attackers gain entry into your computer. They access sensitive information, track your purchasing or search habits, even force your computers perform operations remotely. Current efforts have only proved to be semi effective. Anti-virus software works by comparing your files against a database of known malware. If there is a match, they remove it. However, there is nothing stopping hackers from updating malicious code so that scanners no longer detects them. With each advancement in technology, hackers only become more innovative. It will soon become impossible to predict and prevent hackers from infecting your computer.
If interested in reading more, check out Cliff Stoll's book The Cuckoo's Egg.
