Medical billing inside your EHR or PMS
We work inside the EHR or practice management system you already use, on named accounts your team issues to us after a BAA is signed. Find your system among the 54 below, or tell us if it is not listed.
In short: you keep your EHR and we bill from it, using named accounts with role-based access and two-step login, after a BAA is signed. Pick your system below for its claim form, reports and checks. Nucleus Align has no partnership with any vendor listed.
How do we work inside your EHR or PMS?
We work inside the system you already use, on named accounts your team issues to us, after a Business Associate Agreement (BAA) is signed. You keep your EHR, your records and your clearinghouse. We do not ask you to move to new software.
The access setup is the same for every system on this page:
Our staff complete HIPAA training and sign NDAs, backups we keep are encrypted and automatic, and a dedicated compliance officer owns the program. The security page has the detail.
What do we do once we are in?
We take the billing queues you hand over and work them from charge to payment. Scope is agreed at setup, and it is written down per system because each one splits work differently between charting, billing and the clearinghouse.
- Review charges for missing or mismatched codes, modifiers, diagnosis links and provider details before a claim is built.
- Check eligibility with automated checks before the visit or admission, so coverage problems surface early.
- Run claim edits and send claims through the clearinghouse you already use. Our standard is claims sent within 24 hours of charge entry.
- Post 835 electronic remittance advice (ERA) and match each batch to the bank deposit.
- Work denials from the system's work queues. Our standard is denials worked within 48 hours.
- Follow up on old accounts receivable (A/R) by payer and age, and send patient statements where billing patients is in scope.
For coding rules we use the medical coding service on the same account, and denial trends feed back to charge entry through denial management.
From the system we pull reports by purpose rather than by menu name: charge lag, claim status, A/R aging by payer, denial trends and payment variance. Each system names and builds these differently, so the individual pages say what the vendor documents and we confirm the rest at setup.
How do I pick the right system page?
Find your system in the grid above and open its guide. Each guide covers the claim form the system produces, where access is set, which reports we pull and the checks we run for it. If your system has no guide yet, start with the group that matches your setting below.
| If you are | Start with | Main claim forms |
|---|---|---|
| A hospital or health system | Epic, Oracle Health, MEDITECH, Altera Digital Health, TruBridge or Azalea Health | UB-04 for facility claims, CMS-1500 for professional claims |
| An ambulatory group or independent practice | athenahealth, eClinicalWorks, NextGen Healthcare, Greenway Health, AdvancedMD, Tebra and others | CMS-1500 |
| An urgent care network | Experity or UrgentIQ | CMS-1500, plus UB-04 where a site bills facility claims |
| A specialty practice | ModMed | Set by the specialty and the payer |
| A therapy practice | WebPT or CentralReach | CMS-1500 |
Hospitals and urgent care networks usually run more than one billing setup at once. Our hospital and facility billing service covers the facility side. The hospitals, emergency departments, urgent care networks and large groups and health systems pages cover who we serve.
What do the system groups cover?
We sort the 54 systems by the care setting they are built for. The filters above use the same groups. A vendor can sell into more than one setting, so a system sits in the group where it is mostly used.
| Group | Systems in it | What changes for billing |
|---|---|---|
| Hospital | 6 systems | Facility claims on the UB-04 need bill type, revenue codes and patient status, and professional claims go on the CMS-1500. |
| Ambulatory | 27 systems | Professional claims on the CMS-1500. Each page says where the system documents claim setup. |
| Urgent care and ER | 2 systems | Professional claims, and facility claims where a site bills them. Each page says what the vendor documents. |
| Behavioral health | 6 systems | Professional claims on the CMS-1500. Each page says what the vendor documents. |
| Therapy | 2 systems | Professional claims on the CMS-1500. Each page says what the vendor documents. |
| Specialty | 9 systems | Claim setup follows the specialty. Each page says what the vendor documents. |
| Post-acute | 3 systems | Pages for these systems are being written. We confirm claim form and remittance setup at onboarding. |
Each group row is a summary of how the work usually differs, not a statement about any one vendor. The system pages are where vendor facts live, each tied to the vendor's own pages or an official rule.
How do we handle billing in your system?
We agree the scope and the reports with you at setup, then work from named accounts with two-step login. Charges are checked, claims go out within 24 hours of charge entry, and denials are worked within 48 hours.
If a system does not export something we need, such as a claim in UB-04 form or a remittance file, we say so at setup and agree how to get the data another way. Our revenue cycle management service sets out the full process, and eligibility verification runs ahead of every claim.
Nucleus Align has no partnership, reseller status or endorsement with any vendor named on this page. Vendor and product names are used only to say which system you work in. To talk through your system, book a call.
We check every rule, code and deadline against the official source. See our editorial policy.
Common questions
Straight answers from the team that does the work.
Ask a billing lead directly. A 20-minute call, Monday to Friday, 9am to 5pm Eastern.
01Which EHR systems does a medical billing company need to support?
It needs the system your claims start in, plus the clearinghouse and payer portals around it. We list 54 EHR and practice management systems by care setting, and each has its own page or tile. What matters most is whether we can get named, role-based logins and pull claims, remittances and reports from it.
02Do I have to change my EHR to outsource billing?
No. We work inside the EHR or practice management system you already use, on named accounts your administrator creates after a BAA is signed. You keep your records and your clearinghouse. If something you need cannot be exported from your system, we say so at setup and agree another way to get it.
03Do hospitals and ERs need a different billing setup than small practices?
Yes. Hospital and ER billing adds facility claims on the UB-04, where bill type, revenue codes and patient status must be right, alongside professional claims on the CMS-1500. Many users and sites also share one system. See our hospital and facility billing service and the hospitals page.
04Which EHRs are most common in hospitals and in urgent care?
We do not publish market share rankings, because we have no source for them. What we can say is how we group systems: Epic, Oracle Health, MEDITECH, Altera Digital Health, TruBridge and Azalea Health sit in the hospital group, and Experity and UrgentIQ in urgent care. Each has its own guide.
05What access do you need in my EHR, and how is it protected?
We need a named user account for each team member, with role-based access to billing screens and reports only. Two-step login is on every account, shared logins are not allowed, and a BAA comes first. Our staff are HIPAA trained and sign NDAs. Details are on the security page.
06What if my EHR is not listed?
Tell us which system it is. We confirm at setup what it can export, how claims leave it and how remittances come back, then agree scope and reports in writing. Systems not listed here are not ruled out. Book a call and we will talk through your setup.
07Do you have a partnership with any EHR vendor?
No. Nucleus Align has no partnership, reseller status, certification or endorsement from any vendor listed here. Vendor and product names are plain text so you can find your system. We work as an outside billing team inside the account you own.
Using a system not listed?
Tell us which one. We confirm at setup what it can export, then agree scope and reports with you.