The Importance of a Malware Free System
The integrity of the host is a critical part of the system's Trusted Computing Base. If the host system is compromised by malware so is every Whonix virtual machine, Tor process and communication thought to be anonymous. Malware has malicious intent and can potentially:
- View and take snapshots of your desktop;
- Peruse files and folders;
- Gain access to protected data when decrypted;
- Exfiltrate, corrupt or destroy data (particularly financial and personal information);
- Damage operating system functionality;
- Encrypt the contents of your drive(s) and demand payment for decryption (ransomware);
- Display unwanted advertising;
- Install unwanted software;
- Install persistent rootkits or backdoors;
- Track browsing and other behaviour;
- Remotely turn on webcams and microphones;
- Use your "zombie" computer as part of a botnet for spam email, DDOS attacks or the hosting of illicit / illegal material; and
- Record everything you type, send and receive.
The Utility of Antivirus Tools
Antivirus products and personal firewalls are not drop in solutions for a secure host. Malware can often stay undetected and evade scans, while application level personal firewalls are often circumvented.  Polymorphic code and rootkits essentially render antivirus products helpless.  
Antivirus tools are actually worse than useless. In the case of sophisticated and targeted attacks, the antivirus software can serve as a pathway to exploiting a system's kernel, since they almost always run with administration level privileges. Antivirus software also harms your privacy by sending system files back to the company servers for analysis. The software also actively conducts man-in-the-middle attacks on secure SSL connections, enabling very sensitive information to be viewed.
Preventing Malware Infections
The optimal scenario is to not get infected by malware in the first place. Once malicious code has accessed a system, it is next to impossible to contain. Sensible steps include: hardening the operating system, carefully vetting programs and files that are retrieved from the internet, and using hypervisors (virtualizers) to isolate software that processes untrusted data.
Detecting Malware Infections
Detecting off-the-shelf (standardized) malware is a very hard problem and conceptually a lost cause. If uncustomized malware is widespread enough, then it has a chance of being detected by a technician. Tailored malware might also get detected by a technician, but the likelihood is low unless they are lucky or gifted.
Non-technical users don't have many good options. You can either:
- Spend a few years to rapidly increase your knowledge base of operating systems, network protocols, package analysis, programming, disassembly etc., and then try your luck;
- Pay exorbitant sums to a technician to try and find system malware, even though there is no certainty of success; or 
- Seek the voluntary assistance of a technician to find malware, if you are both a high value target and have a reasonable rationale for why you are likely compromised.